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Bienvenue à Babylon Floral Design, la boutique de fleurs Denvers la plus unique, spécialisée dans le design floral de pointe et des articles-cadeaux uniques. Nous nous efforçons de fournir les arrangements et le service les plus exquis pour des individus et des événements en transformant des pensées et des sentiments dans l'art floral, employant la couleur, la texture, la forme et le style pour communiquer. N'hésitez pas à parcourir notre galerie et notre blog pour avoir une idée de ce que nous faisons et visiter notre page de commande pour connaître notre approche unique pour commander des fleurs. Nous sélectionnons à la main nos fleurs tous les jours et portons un grand assortiment d'orchidées fraîches et tropicales avec des pics saisonniers. Pour les demandes spéciales, appelez la veille et bien commander ce que vous voulez. Nous sommes heureux d'offrir une livraison à travers la ville et une association avec un consortium de fleuristes de qualité, offrant un design floral exceptionnel pour la livraison nationale et internationale. Si vous souhaitez effectuer un achat et que votre adresse de facturation et / ou votre carte de crédit est en dehors des États-Unis, veuillez appeler la boutique pour commander. Nous fournissons des commandes sécurisées en ligne 24 heures par jour, mais nous ne livrons pas le dimanche ou la plupart des grands jours fériés. Babylon Floral 1223 East 17th Ave. Denver, CO 303.830.6855Liste alphabétique des instructions SHELXL Liste alphabétique des instructions SHELXL Les instructions suivantes peuvent être utilisées dans le manuel. Ins pour SHELXL. Les valeurs par défaut sont indiquées entre crochets indiquant que le programme générera une valeur par défaut appropriée basée sur le reste des informations disponibles. Les lignes de prolongation sont signalées par à la fin d'une ligne, l'instruction étant poursuivie sur la ligne suivante qui doit commencer par un ou plusieurs espaces. Les autres lignes commençant par des espaces sont traitées comme des commentaires, de sorte que des lignes vides peuvent être ajoutées pour améliorer la lisibilité. Tous les caractères qui suivent ou dans une ligne d'instruction sont ignorés. Les instructions SHELXL-97 TIME, HOPE et MOLE ont été déconseillées. Le . Ins peut inclure une instruction de la forme: filename (le caractère doit être dans la colonne 1). Cela entraîne la saisie supplémentaire à partir du fichier nommé jusqu'à ce qu'une instruction END est rencontrée dans ce fichier, après quoi le fichier est fermé et les instructions sont prises à partir de la ligne suivante de la. Ins. Les instructions d 'entrée d' un tel fichier d 'inclusion ne sont pas répercutées dans le fichier. Lst et. Rés, et ne peut pas contenir FVAR. BASF. EXTI ou SWAT ou des atomes (sauf dans une section FRAG. FEND) car cela empêcherait les. Res d'être utilisé inchangé pour le travail de raffinement suivant (après avoir renommé comme. Ins). Cette installation est principalement destinée à de longues listes de contraintes et d'instructions LAUE qui seraient les mêmes pour chaque raffinement d'une structure donnée. Filename lit également les instructions du fichier nommé, mais les copie dans le fichier. res le cas échéant. Ces fichiers d'inclusion peuvent appeler d'autres fichiers à l'aide de filename, mais pas de nom de fichier. Filename est répercuté dans le fichier. res s'il est dans le fichier. ins mais pas s'il est dans un fichier ou, le nom de fichier n'est jamais répercuté. Le fichier. ins doit toujours commencer par TITL. CELLULE. ZERR. LATT, SYMM. NEUT, SFAC. DISP et UNIT dans cet ordre et terminez avec HKLF et END. Les instructions entre crochets ne sont pas toujours requises. Il peut y avoir plus d'un SYMM. SFAC et DISP. Les instructions Atom commencent par un nom d'atome (jusqu'à 4 caractères, dont le premier doit être une lettre) qui ne correspondent à aucune des instructions SHELXL, et terminé par au moins un blanc) suivi d'un numéro de facteur de diffusion qui se réfère à La liste définie par les instructions SFAC, x, y et z en coordonnées fractionnaires et (facultativement) un facteur d'occupation du site (sof) et un isotrope U ou six composantes anisotropes U ij (dans Aringsup2). Notez que différents systèmes de programmes peuvent différer dans leur ordre de composantes U ij Le facteur exponentiel prend la forme exp (-8pisup2Usin (theta) lambdasup2) pour un paramètre de déplacement isotrope U et: exp (-2pisup2 hsup2 (a) sup2U 11 ksup2 (b ) Sup2U 22 .2hkabU 12) pour anisotropes U ij. Un atome est spécifié comme suit dans le fichier. Ins: nom atomique sfac x y z sof11 U0.05 ou U 11 U 22 U 33 U 23 U 13 U 12 La combinaison des numéros d'atom, PART et RESI doit être unique. Pour fixer n'importe quel paramètre atomique, ajoutez 10. Ainsi, le facteur d'occupation du site est normalement donné comme 11 (c'est-à-dire fixé à 1). Le facteur d'occupation du site pour un atome en position spéciale doit être multiplié par la multiplicité de cette position (comme indiqué dans les tableaux internationaux, volume A) et divisé par la multiplicité de la position générale pour ce groupe d'espace. Par exemple, un atome sur un axe quadruple aura habituellement 10,25 en position sof. Si tout paramètre atomique est donné comme (10bullmp), où abs (p) est inférieur à 5 et m est un entier, il est interprété comme pbullfv m. Où fv m est la mth variable libre (voir FVAR). Notez qu'il n'y a pas de fv 1. puisque cette position sur une instruction FVAR est occupée par le facteur d'échelle global et m1 correspond à la fixation d'un atome en ajoutant 10. Si m est négatif, le paramètre est interprété comme pbull (1-fv m ). Ainsi, pour contraindre deux facteurs d'occupation à ajouter 0,25 (pour deux éléments occupant la même position spéciale quadruple), ils pourraient être donnés comme 20,25 et -20,25, soit 0,25bullfv 2 et 0,25bull (1-fv 2), ce qui correspond à p0 0,25, m2 et p-0,25, m-2 respectivement. Dans SHELX-76, il a été nécessaire d'utiliser des variables libres et de coordonner la fixation de cette manière pour établir les contraintes appropriées pour le raffinement des atomes sur des positions spéciales. Dans SHELXL, ceci est autorisé (pour la compatibilité ascendante) mais n'est pas recommandé: le programme établira automatiquement et appliquera les contraintes appropriées positionnelles, sof et U ij pour n'importe quelle position spéciale dans n'importe quel groupe d'espace, dans un arrangement conventionnel ou autrement. Si l'utilisateur applique (correcte ou incorrecte) des contraintes de position spéciales en utilisant des variables libres, etc., le programme suppose que cela a été fait avec intention et signale, mais n'applique pas les contraintes correctes. Ainsi, l'application accidentelle d'une variable libre à un U ij terme d'un atome sur une position spéciale peut conduire à l'affinement soufflage Tout ce qui est nécessaire est de spécifier atomname, sfac, x, y et z, et laisser le reste à la Lorsque l'atome est (plus tard) rendu anisotrope en utilisant la commande ANIS, les contraintes U ij appropriées seront ajoutées par le programme. Si sof est laissé de côté, il sera fixé à la valeur appropriée de 1 pour une position générale et de moins de 1 pour une position spéciale. Étant donné que SHELXL génère automatiquement des restrictions d'origine pour les groupes d'espace polaires, aucune coordonnée d'atomes ne doit être fixée par l'utilisateur à cette fin. Il peut encore être nécessaire d'appliquer des contraintes à la main pour traiter le désordre. Un cas commun est quand il y a deux positions possibles pour un groupe d'atomes, dans lequel le premier ensemble devrait avoir tous les sofs de (disons) 21 et le second ensemble -21 , De sorte que la somme des deux facteurs d'occupation est fixée à 1, mais que les valeurs individuelles peuvent affiner comme fv 2 et 1-fv 2. De même, si une position spéciale de symétrie 2m est occupée par Ca 2 et Ba 2, Deux ions pourraient être donnés les sofs 30,25 et -30,25 respectivement. Dans ce cas, il serait souhaitable d'utiliser l'instruction EADP pour égaliser les paramètres de déplacement Ca 2 et Ba 2 (anisotropes). Si un U isotrope est donné comme - T, où T est dans la gamme de 0,5 lt T lt 5, il est fixé à T fois l'U eq de l'atome précédent non restreint de cette manière. La valeur U résultante n'est pas affinée indépendamment, mais est mise à jour après chaque cycle de moindres carrés. Lit h, k, l, A et B à partir du fichier nom. fab. Où A et B sont les composantes réelles et imaginaires d'un facteur de structure partielle. Ce fichier est lu en format libre (nombres séparés par un ou plusieurs espaces) avec une réflexion par ligne, et se termine par la fin du fichier, une ligne vierge ou une réflexion fictive 0,0,0. Toutes les informations suivantes dans ce fichier sont ignorées et peuvent être utilisées pour les commentaires. Les réflexions peuvent être dans n'importe quel ordre, les doublons et les absences systématiques sont ignorées. Les équivalents de symétrie sont générés automatiquement. Au moins un équivalent de chaque réflexion utilisée dans le raffinement, y compris toutes les réflexions dans toutes les composantes jumelles, devrait être présent dans cette liste, les réflexions superflues dans le fichier. fab (par exemple en dehors des limites de résolution) sont ignorées. Dans le cas du jumelage, les valeurs A et B doivent se référer à la structure non tentée, mais elles sont utilisées pour calculer les facteurs de structure pour toutes les composantes jumelles. Ainsi, le fichier. fcf créé à l'aide de la nouvelle LIST 8. Qui a déjà été détendue et fusionnée (en utilisant la loi de Friedels uniquement pour les structures centrosymétriques) mais qui contient encore les contributions anormales, peut être utilisé comme une aide pour les générer. Les valeurs d'entrée A et B sont multipliées par k. exp (-8pisup2Usinsup2thetalambdasup2), où k est la valeur de la variable libre n 1 et U la valeur de la variable libre n 2. Si n 2 est omis, U est mis à zéro, Et si n 1 est également omis, k est fixé à 1,0 (auquel cas les valeurs A et B devraient être sur une échelle absolue d'électrons par unité de cellule). Les contraintes SUMP peuvent être appliquées à ces variables libres. Les contributions au facteur de structure partielle pourraient provenir d'un masque de solvant (pour une macromolécule) ou d'une goutte de densité de solvant non résolue pour une petite molécule, par ex. Dans un canal le long d'un axe de cellule, tel que modélisé par la méthode de compression dans PLATON. Dans ce dernier cas, il pourrait être approprié de fixer le troisième L. S. Paramètre au nombre de paramètres qui auraient été nécessaires pour modéliser une telle région de solvant en lui ajustant des molécules de solvant désordonnées, de sorte que les incertitudes standard sont estimées correctement. N1 peut être rendu négatif pour forcer le programme à ne pas assumer la loi de Friedels lorsqu'il génère des équivalents des valeurs A et B d'entrée, ceci n'est nécessaire que lorsque les facteurs de structure partielle ont des contributions anormales significatives. Un fichier CIF est écrit dans. cif pour l'archivage et la vérification. ACTA définit automatiquement le BOND. FMAP 2, MERG 2, PLAN et LIST 4, et ne peut être utilisé avec d'autres FMAP. MERG ou LIST ou avec un seuil d'OMIT positif. Un message d'avertissement s'affiche si le contenu de la cellule de l'instruction UNIT n'est pas cohérent avec la liste des atomes, car ils sont utilisés pour calculer la densité, etc. Fichier de sortie CIF. 2theta full est utilisé pour spécifier la valeur de 2theta pour laquelle le programme calcule l'intégralité des données. La valeur par défaut est la valeur 2theta à laquelle sin (theta) lambda0.6. En outre, l'intégralité est calculée jusqu'à la valeur maximale de 2theta pour les données de réflexion. SHELXL ignore les absences systématiques et la réflexion 0,0,0 dans le calcul de l'intégralité. Deux mots-clés peuvent apparaître sur l'instruction ACTA en plus des paramètres numériques. NOHKL désactive l'encapsulation par défaut de la. Res. Fab et. Hkl dans le. Fichier CIF. Cela ne doit être utilisé que pour de bonnes raisons, p. Car le fichier CIF est destiné à l'entrée dans un programme graphique qui a des problèmes avec les fichiers d'entrée de grande taille. Il est scientifiquement très souhaitable que les données complètes soient déposées et archivées. Le keword TABS attache a aux noms d'atomes dans PARTIE 1, b aux noms d'atom dans la PARTIE 2 etc. exactement comme employé dans. Lst fichier. Cela facilite la compréhension des listes des longueurs et angles des liaisons, en particulier si les mêmes noms d'atomes sont utilisés pour différents composants de désordre (pratique standard en format PDB). L'utilisation du mot-clé TABS peut faire que les noms d'atomes deviennent trop longs pour certains programmes. AFIX mn d sof11 U10.08 AFIX applique des contraintes et génère des coordonnées idéalisées pour tous les atomes jusqu'à ce que la prochaine instruction AFIX soit lue. Les chiffres mn du code AFIX contrôlent deux opérations logiquement assez distinctes. M désigne des opérations géométriques qui sont effectuées avant le premier cycle de raffinement (les atomes d'hydrogène sont idéalisés avant chaque cycle), et n établit des contraintes qui sont appliquées tout au long du raffinement des moindres carrés. N est toujours un seul chiffre m peut être deux, un ou zéro chiffre (le dernier correspond à m0). Les options pour l'idéalisation des positions d'atomes d'hydrogène dépendent de la table de connectivité configurée à l'aide de CONN. LIER. FREE et PART this peut également être utilisé pour générer des atomes d'hydrogène attachés à des groupes désordonnés et à des atomes sur des positions spéciales. D détermine les longueurs de liaison dans les groupes idéalisés, et sof et U remplacent les valeurs dans la liste d'atomes pour tous les atomes jusqu'à la prochaine instruction AFIX. U n'est pas appliqué si l'atome est déjà anisotrope, mais est utilisé si un atome isotrope doit être anisotrope en utilisant ANIS. Toute valeur U légale peut être utilisée, par ex. 31 (une variable de référence libre) ou -1,2 (1,2 fois U eq de l'atome normal précédent). Chaque instruction AFIX doit être suivie du nombre requis d'hydrogène ou d'autres atomes. Bien que les instructions AFIX soient destinées à la mise en place d'atomes d'hydrogène, il est également possible d'utiliser AFIX 30, 120 ou 130 pour établir des groupes CF 3 idéaux. Cependant, ceux-ci ne peuvent pas être raffinés avec un modèle d'équitation parce que les atomes de fluor apportent une contribution beaucoup plus grande aux facteurs de structure calculés que l'atome de carbone le raffinement serait instable. L'utilisation de DFIX ou SADI est recommandée, par ex. Noter la contrainte SADI relativement douce à l'atome suivant pour permettre au groupe CF 3 de s'incliner un peu. En variante, s'il n'y a pas de deuxième conformation, un groupe rigide AFIX 6 ou AFIX 9 peut être utilisé. L'instruction SADI ci-dessus peut être ajoutée si nécessaire. Les options AFIX individuelles sont les suivantes: les distances X-H par défaut dépendent à la fois de l'environnement chimique et de la température (pour permettre les effets libraires) qui est spécifiée au moyen de l'instruction TEMP. M1 C-H tertiaire idéalisé avec tous les angles X-C-H égaux. Il doit y avoir trois et seulement trois autres liaisons dans la table de connectivité à l'atome immédiatement précédent. M1 est souvent associé à un raffinement de modèle d'équitation (n3). M2 CH 2 idéalisé avec tous les angles X-C-H et Y-C-H égaux, et H-C-H déterminé par X-C-Y (c'est-à-dire approximativement tétraédrique, mais élargi si X-C-Y est inférieur à tétraédrique). Cette option est également adaptée à un raffinement équestre (n3). M3 Groupe CH 3 idéal avec des angles tétraédriques. Le groupe est décalé par rapport à la plus courte autre liaison à l'atome auquel le groupe-CH 3 est attaché. S'il n'y a pas de telle liaison (par exemple une molécule de solvant d'acétonitrile) cette méthode ne peut pas être utilisée (mais m13 est encore viable). M4 C-H ou amide aromatique N-H avec l'hydrogène sur la bissectrice externe de l'angle X-C-Y ou X-N-Y. M4 est approprié pour un raffinement de modèle d'équitation, c'est-à-dire AFIX 43 avant l'atome de H. M5 Cinq atomes de non-hydrogène suivants sont montés sur un pentagone régulier, par défaut d1.42 Aring. M6 Les six atomes de non-hydrogène suivants sont montés sur un hexagone régulier, par défaut d1.39 Aring. M7 Actuellement identique à m6, réservé à une autre utilisation dans le futur (par exemple OH 2). M8 Groupe OH idéal, avec angle X-O-H tétraédrique. Si l'oxygène est attaché à un carbone saturé, les trois positions décalées sont considérées pour l'hydrogène. Si elle est attachée à un anneau aromatique, les deux positions dans le plan sont considérées. Le choix final est basé sur la formation de la meilleure liaison hydrogène avec un atome d'azote, d'oxygène, de chlore ou de fluor. L'algorithme implique la génération d'une position potentielle pour un tel atome en extrapolant le vecteur O-H, puis en trouvant l'atome de N, O, F ou Cl le plus proche dans cette position, en tenant compte des équivalents de symétrie. Si un autre atome qui (selon la table de connectivité) est lié à l'atome N, O, F ou Cl, est plus proche de la position idéale, l'atome N, O, F ou Cl n'est pas considéré. M9 Terminal idéalisé XCH 2 ou XNH 2 avec les atomes d'hydrogène dans le plan du substituant le plus proche sur l'atome X. Convient pour le raffinement du modèle d'équitation (AFIX 93 avant les deux atomes de H). M10 Pentaméthylcyclopentadiényle idéalisé (Cp). Cet AFIX doit être suivi des 5 atomes de carbone du cycle puis des 5 atomes de carbone méthyle dans l'ordre cyclique, de sorte que le premier groupe méthyle (atome 6) est lié au premier atome de carbone (atome 1). La valeur par défaut d est 1.42 Aring, avec la distance C-CH 3 réglée à 1.063d. Un raffinement de groupe rigide variable métrique (AFIX 109) serait approprié et permettrait un raccourcissement libationnel des liaisons. Les atomes d'hydrogène (par exemple avec AFIX 37 ou 127) peuvent être inclus après les atomes de carbone correspondants, auquel cas AFIX 0 ou 5 (dans le cas d'un raffinement de groupe rigide) doit être inséré avant le prochain atome de carbone. M11 Groupe naphtalène idéalisé avec des liaisons égales (défaut d1.39 A). Les atomes doivent être numérotés comme une figure symétrique de huit, commençant par l'alpha C et suivis par le bêta, de sorte que les six premiers atomes (et aussi les six derniers) décrivent un hexagone dans l'ordre cyclique. M11 est également approprié pour le raffinement de groupe rigide (AFIX 116). M12 Groupe méthyle désordonné idéalisé en m3 mais avec deux positions pivotées l'une par rapport à l'autre de 60 degrés. Les facteurs d'occupation correspondants doivent normalement être fixés pour ajouter jusqu'à un, par exemple, En les donnant comme 21 i. e. 1fv 2 et -21 1 (1-fv 2). Si HFIX est utilisé pour générer une instruction AFIX avec m12, les facteurs d'occupation sont fixés à 0,5. AFIX 12n est approprié pour un para méthyle sur un groupe phényle sans substituants méta, et doit être suivi de 6 demi-atomes d'hydrogène (les trois premiers pour un composant - CH 3, puis les trois pour l'autre, de sorte que les hydrogènes n et n3 Sont en face l'une de l'autre). Les six atomes d'hydrogène doivent avoir le même numéro de PART que le carbone auquel ils sont attachés (par exemple PARTIE 0). M13 Groupe CH 3 idéal avec des angles tétraédriques. Si les coordonnées du premier atome d'hydrogène sont non nulles, elles définissent l'angle de torsion du groupe méthyle. Sinon (ou si l'instruction AFIX est générée via HFIX), un calcul de facteur de structure est effectué sans les atomes d'hydrogène et l'angle de torsion est établi qui maximise la somme des densités de différence aux trois positions d'hydrogène. Ceci est habituellement suivi d'un raffinement de l'angle de torsion (AFIX 137). M14 Groupe OH idéal, avec angle X-O-H tétraédrique. Si les coordonnées de l'atome d'hydrogène sont non nulles, elles sont utilisées pour définir l'angle de torsion. Sinon (ou si HFIX a été utilisé pour configurer l'instruction AFIX), l'angle de torsion est choisi pour maximiser la densité électronique (voir m13). Etant donné que cet angle de torsion est peu probable pour être très précis, l'utilisation d'un raffinement de groupe rotatif est recommandée (c'est-à-dire AFIX 147 avant l'atome H). M15 groupe BH dans lequel l'atome de bore est lié à quatre ou cinq autres atomes comme partie d'un fragment polyédrique. L'atome d'hydrogène est placé sur le vecteur qui représente la somme négative des vecteurs unitaires le long des quatre ou cinq autres liaisons à l'atome de bore. M16 C-H acétylénique, avec X-C-H linéaire. Habituellement raffiné avec le modèle d'équitation, c'est-à-dire AFIX 163. mgt16 Un groupe défini dans un FRAG. La section FEND avec codem est installée, habituellement comme préliminaire à un raffinement de groupe rigide. Le FRAG. La section FEND doit précéder l 'instruction AFIX correspondante dans le fichier. Ins, mais il peut y avoir n'importe quel nombre d'instructions AFIX avec le même m correspondant à un seul FRAG. FEND. Lorsqu'un groupe est monté (m5, 6, 10 ou 11, ou mgt16), des atomes avec des coordonnées non nulles sont utilisés comme des atomes cibles de poids égal. Les atomes avec les trois coordonnées zéro sont ignorés. On peut utiliser trois ou plusieurs atomes non colinéaires comme atomes cibles. Les équidés (n3,4) et les atomes d'hydrogène en rotation (n7,8), mais pas les autres groupes idéalisés, sont ré-idéalisés (si m est 1, 2, 3, 4, 8, 9, 12, 13, 14, 15 ou 16) avant chaque cycle de raffinement (après le premier cycle, les coordonnées du premier hydrogène d'un groupe sont toujours non nulles, de sorte que l'angle de torsion est retenu lors de la ré-idéalisation). Pour n4 et 8, les angles sont ré-idéalisés, mais la longueur de la liaison XH (raffinée) est retenue, à moins que les coordonnées de l'hydrogène ne soient toutes nulles, auquel cas d (sur l'instruction AFIX) ou (si d n'est pas donné) Valeur qui dépend de l'environnement chimique et la température (TEMP) est utilisé à la place. N1 Les coordonnées, sof et U ou U ij sont fixes. N2 Le sof et U (ou U ij) sont fixes, mais les coordonnées sont libres d'affiner. N3 Les coordonnées, mais pas le sof ou U (ou U ij), roulent sur l'autre atome précédent. Les mêmes décalages sont appliqués aux coordonnées des deux atomes, et les deux contribuent au calcul de la dérivée. L'atome sur lequel l'équitation est effectuée ne peut pas être lui-même un atome d'équitation, mais il peut être dans un groupe rigide (n5,6 ou 9). N4 Cette contrainte est la même que n3, sauf que la distance X-H est libre d'affiner. La direction du vecteur X-H ne change pas. Cette contrainte nécessite des données de réflexion de meilleure qualité que n3, mais permet des variations dans les distances X-H apparentes causées par les effets de libration et de liaison. S'il y a plus d'un hydrogène équivalent, on applique le même décalage à chaque distance X-H équivalente (par exemple à toutes les trois liaisons C-H dans un groupe méthyle). N4 peut être combiné avec des contraintes DFIX ou SADI (pour restreindre des distances XH chimiquement équivalentes pour être égales) ou incorporé à l'intérieur d'un groupe rigide (n6), auquel cas l'atome suivant (le cas échéant) dans le même groupe rigide doit suivre un AFIX explicite Instruction avec n5. N5 Le ou les atomes suivants sont des atomes dépendant d'un groupe rigide. Ceci est généré automatiquement pour les atomes suivant un atome n6 ou n9, de sorte qu'il n'est pas nécessaire d'être spécifiquement inclus sauf si m doit être changé (par exemple AFIX 35 avant le premier hydrogène d'un groupe méthyle rigide avec AFIX 6 ou 9 avant le carbone précédent ). N6 L'atome suivant est l'atome de pivot d'un nouveau groupe rigide, c'est-à-dire que les autres atomes du groupe rigide tournent autour de cet atome et que les mêmes déplacements de translation sont appliqués à tous les atomes du groupe rigide. N7 Les atomes suivants (habituellement hydrogène) (jusqu'au prochain AFIX avec n non égal à 7) sont autorisés à monter sur l'atome X immédiatement précédent et tourner autour de la liaison YX X doit être lié à un et un seul atome Y dans la connectivité Liste, en ignorant les atomes n7 (qui, s'ils sont F plutôt que H, peuvent être présents dans la liste de connectivité). Le mouvement des atomes de ce groupe en rotation est une combinaison de mouvement d'équitation (c. f. n3) sur l'atome X plus une composante tangentielle perpendiculaire aux liaisons Y-X et X-H, de sorte que les distances X-H, Y-X-H et H-X-H demeurent inchangées. Cette contrainte est destinée aux groupes - OH, - CH 3 et éventuellement - CF 3. X peut faire partie d'un groupe rigide, qui peut être repris avec un AFIX n5 suivant les atomes n7. N8 Cette contrainte est similaire à n7, sauf que les distances X-H peuvent également varier, les mêmes décalages étant appliqués à toutes les liaisons X-H au même atome. Ainsi, seuls les angles Y-X-H et H-X-H sont maintenus constants, la relation de n8 à n7 correspond à celle de n4 à n3. Les restrictions DFIX et SADI peuvent être utiles pour les distances X-H. Cette contrainte est utile pour les groupes - CF 3 ou pour les groupes - CH 3 avec de bonnes données. N9 Le premier atome (pivot) d'un nouveau groupe rigide métrique variable. Un tel groupe conserve sa forme mais peut se contracter ou se dilater uniformément. Il est utile pour les groupes C 5 H 5 et BF 4, qui peuvent montrer un raccourcissement librationnel appréciable des longueurs de liaison. Les atomes suivants dans ce type de groupe rigide devraient avoir n5, qui est généré automatiquement par le programme si aucune autre instruction AFIX n'est insérée entre les atomes. Les atomes d'équitation ne sont pas autorisés à l'intérieur de ce type de groupe rigide. Seules les coordonnées des atomes de pivotement peuvent être fixées (en ajoutant 10) ou liées à des variables libres, et seul l'atome de pivot peut reposer sur une position spéciale. Un groupe rigide ou un ensemble d'hydrogènes dépendants doit toujours être suivi par AFIX 0 (ou une autre instruction AFIX). Laisser AFIX 0 par erreur est une cause commune d'erreur, le programme est capable de détecter certains cas évidents, mais dans de nombreux cas ce n'est pas logiquement possible. Les n atomes isotropes non isothermes suivants sont rendus anisotropes, générant des contraintes de position particulières appropriées pour le U ij si nécessaire. Les atomes intervenants qui sont déjà anisotropes ne sont pas comptés. Un négatif n a le même effet. Les atomes nommés sont rendus anisotropes (sinon déjà), générant les contraintes appropriées pour des positions spéciales. Notez que les noms peuvent inclure suivi d'un nom de facteur de diffusion (voir SFAC) ANIS CL rendrait tous les atomes de chlore anisotropes. Comme ANIS, comme d'autres instructions, s'applique au résidu courant, sauf indication contraire, ANIS S devrait rendre les atomes de soufre dans tous les résidus anisotropes (par exemple). ANIS doit précéder les atomes auxquels il doit être appliqué. ANIS seul, n'ayant ni nombre ni noms en tant que paramètres, rend tous les atomes suivants non hydrogène (dans tous les résidus) anisotropes. Le L. S. Et les instructions CGLS offrent la possibilité de retarder la conversion en anisotropes de tous les atomes spécifiés par ANIS jusqu'à ce qu'un nombre donné de cycles de moindres carrés ait été effectué. ANSC six coefficients Applique la mise à l'échelle anisotrope. Ce n'est que d'habitude une utilisation pratique pour des raffinements isotropes de macromolécules, car il serait corrélé avec les ADP anisotropes individuels, bien qu'il puisse être applicable dans les cas où seuls les atomes lourds sont raffinés anisotropiquement. Dans le premier travail, l'ANSC est entré sans aucun paramètre dans la première exécution et est écrit dans le fichier. res avec six paramètres et peut être réintroduit pour le raffinement suivant. Bien que six paramètres soient nécessaires, le programme applique automatiquement les contraintes appropriées pour le système de cristaux, si habituellement moins de six paramètres sont réellement affinés. Anres est l'esd d'une contrainte qui est appliquée avec des valeurs cibles de zéro aux six paramètres ANSC pour empêcher des instabilités en raffinement de pleine matrice, en particulier lorsque tous les atomes sont également raffinés anisotropiquement, ce qui introduirait des corrélations de 100. Cette instruction sera rarement Nécessaire, car la valeur de limitation par défaut est généralement suffisante. Facteurs d'échelle BASF Les facteurs d'échelle de lot relatifs sont inclus dans le raffinement des moindres carrés basé sur les numéros de lot dans le fichier. hkl. Pour le numéro de lot BN, la valeur F c sup2 est multipliée par le facteur d'échelle (BN-1) de l'instruction BASF, ainsi que par le facteur d'échelle global. Pour le lot n ° 1 (ou zéro), F c est multiplié par le facteur d'échelle global, mais pas par un facteur d'échelle de lot. La matrice des moindres carrés sera singulière s'il n'y a pas de réflexions avec BN1 (ou zéro), donc le programme considère qu'il s'agit d'une erreur. Notez que les facteurs d'échelle BASF, contrairement au facteur d'échelle global (voir FVAR), sont relatifs à Fsup2 et non pas F. Pour les cristaux jumelés, c'est-à-dire lorsque TWIN ou HKLF 5 sont utilisés, BASF spécifie les contributions en volume fractionnaire des différents composants jumeaux. Le programme permet désormais aux paramètres BASF de devenir négatifs, bien que, bien sûr, ils doivent toujours être positifs. BIND atom1 atom2 La liaison spécifiée (qui peut être de n'importe quelle longueur) est ajoutée à la liste de connectivité si elle n'est pas déjà là. Un seul des deux atomes peut être un atome équivalent (c'est-à-dire avoir l'extension n). Les atomes de la PARTIE m peuvent se lier aux atomes de la PARTIE n. Cela étend les règles PARTIE et permet de définir les PARTIES au sein de PARTIES. Ces chiffres peuvent être positifs ou négatifs. BLOC n1 n2 atomnames Si n1 ou n2 sont positifs, les paramètres x, y et z des atomes nommés sont affinés dans le cycle n1 ou n2 respectivement. Si n1 ou n2 sont négatifs, les paramètres d'occupation et de déplacement sont affinés dans le cycle. Pas plus de deux nombres de cycles de ce type ne peuvent être spécifiés sur une seule instruction BLOC, mais les mêmes atomes peuvent être mentionnés dans n'importe quel nombre d'instructions BLOC. Pour affiner à la fois x, y et z ainsi que les paramètres de déplacement d'un atome dans le même bloc, n1 et n2 doivent spécifier le même numéro de cycle, mais avec des signes opposés. Une instruction BLOC sans noms d'atomes s'applique à tous les atomes dans les cycles spécifiés. Le motif des blocs est répété après que le nombre maximum de blocs a été atteint si le nombre de L. S. Les cycles de raffinement sont plus grands que le BLOC maximal n1 ou n2. Si un nombre de cycles inférieur au maximum n1 ou n2 n'est pas mentionné dans une instruction BLOC, il est traité comme une matrice complète. L'échelle globale, les facteurs d'échelle batchtwin, le coefficient d'extinction, les paramètres SWAT et les variables libres (le cas échéant) sont affinés dans chaque bloc. Les atomes d'hydrogène (hydrogène) et les atomes dans les groupes rigides sont inclus dans les mêmes blocs que les atomes sur lesquels ils roulent. Par exemple, un polypeptide composé de 30 résidus (résidu 1..30 fixé par les instructions RESI) pourrait être affiné efficacement comme suit (tous les atomes non hydrogène supposés anisotropes): ce qui assurerait 3 blocs de taille approximativement égale d'environ 800 paramètres chacun Et un certain chevauchement entre les deux blocs anisotropes pour éviter les problèmes où ils se joignent. Les paramètres géométriques affineraient dans les cycles 1,4,7. Et les paramètres de déplacement anisotrope dans les cycles restants. Dans cet exemple, on suppose que le premier atome dans chaque résidu est N et le dernier est O. Une autre bonne stratégie de blocage serait de diviser la structure en trois blocs chevauchants de paramètres xyz et U ij et d'ajouter un quatrième cycle dans (Xyz, sof et U ou U ij) dans tous les paramètres atomiques (xyz, sof et U ou U ij), c'est-à-dire que toutes les valeurs xyz mais pas U ij sont affinées Les cycles spécifiés. Une telle instruction BLOC a priorité sur toutes les autres instructions BLOC, quel que soit leur ordre dans le fichier. ins. Il est important qu'il y ait un chevauchement suffisant entre les blocs pour permettre à chaque esd d'être estimée avec tous les atomes contribuants affinés dans au moins un des cycles de raffinement. BOND produit des longueurs de liaison pour toutes les liaisons (définies dans la liste de connectivité) qui impliquent deux atomes référencés sur la même instruction BOND. Les angles sont produits pour toutes les paires de ces liaisons impliquant un atome commun. Une instruction BOND sans paramètres délivre des longueurs de liaison (et les angles correspondants) pour toutes les liaisons dans la table de connectivité, et BOND H seule comprend toutes les liaisons aux hydrogènes (mais comme les hydrogènes ne sont pas inclus dans la table de connectivité, les liaisons Impliquant des atomes d'hydrogène équivalents de symétrie ne sont pas inclus). D'autres noms d'éléments peuvent également être référencés globalement en les précédant avec une instruction BOND. BOND est réglé automatiquement par ACTA. Et les longueurs et les angles des liaisons sont écrites dans la. Fichier CIF. Notez que la meilleure façon de calculer les angles B-H-B est avec RTAB. Les contraintes anti-chocs sont générées automatiquement pour toutes les distances impliquant deux atomes non liés C, N, O et S (basés sur le type SFAC) qui sont plus courtes que les distances non liées les plus courtes attendues, permettant la possibilité de liaisons hydrogène. Toutes les paires d'atomes qui ne sont pas connectées par une, deux ou trois liaisons dans la table de connectivité sont considérées comme non liées à cet effet. Des contraintes anti-choc sont également générées pour des contacts courts entre des atomes d'hydrogène (le cas échéant) à condition que les deux atomes d'hydrogène ne soient pas liés au même atome, ceci devrait aider à éviter des conformations de chaînes latérales défavorables énergiquement. Si la somme des occupa - tions des deux atomes est inférieure à 1,1, aucune contrainte n'est générée aussi si les atomes ont des numéros de PART différents et qu'aucun d'eux n'est nul, aucune contrainte n'est générée. La valeur par défaut esd s est le premier paramètre DEFS (0,02 s'il n'y a pas d'instruction DEFS). If s is given a negative sign, the absolute value is used as an esd, and symmetry equivalent atoms in the connectivity array are considered too in deciding which atoms are connected and so should not have anti-bumping restraints applied. Thus when s is positive (the default action if s is not specified on the BUMP instruction) short contacts between appropriate atoms in different asymmetric units always result in anti-bumping restraints. This will be the normal procedure for macromolecular refinements (where it helps to eliminate accidental contacts between molecules in low-resolution refinements), but in the (unusual) case of a crystallographic twofold axis running through (say) a disulfide bond it will be necessary to make s negative to prevent the generation of anti-bumping restraints that would break the bond. Refinement with anti-bumping restraints provides a solvent model with acceptable hydrogen bonding distances that is consistent with the diffraction data. The anti-bumping restraints are regenerated before each refinement cycle. Anti-bumping restraints can also be added by hand using DFIX instructions with negative distances d. CELL lambda a b c alpha beta gamma Wavelength and unit-cell dimensions in Aring and degrees. CGLS nls0 nrf0 nextra0 As L. S.. but the conjugate-gradient algorithm is employed instead of the full-matrix approach. Although BLOC may be used with CGLS, in practice it is much better to refine all parameters at once. CGLS is much faster than L. S. for a large number of parameters, and so will be the method of choice for most macromolecular refinements. The convergence properties of CGLS are good in the early stages (especially if there are many restraints), but cannot compete with L. S. in the final stages for structures which are small enough for full-matrix refinement. The major disadvantage of CGLS is that it does not provide standard uncertainties, so that when a large structure has been refined to convergence using CGLS it may be worth performing a blocked full-matrix refinement (L. S.BLOC) to obtain the standard deviations in quantities of interest (e. g. torsion angles, in which case only xyz blocks would be required).The other parameters have the same meaning as with L. S. CGLS is suitable for R free tests (negative nrf). The CGLS algorithm is based closely on the procedure described by Hendrickson amp Konnert Computing in Crystallography (1980) 13.01-13.25. The structure-factor derivatives contribute only to the diagonal elements of the least-squares matrix, but all additional observational equations (restraints) contribute in full to diagonal and off-diagonal terms, although neither the l. s. matrix A nor the Jacobean J are ever generated. The preconditioning recommended by Hendrickson amp Konnert is used to speed up the convergence of the internal conjugate gradient iterations, and has the additional advantage of preventing the excessive damping of poorly determined parameters that is characteristic of other conjugate gradient algorithms Tronrud, Acta Cryst. A48 (1992) 912-916. A further refinement in the CGLS approach is to save the parameter shifts from the previous CGLS cycle, and to use them to improve the estimated parameter shifts in the current cycle. Since this is only possible in the second and subsequent cycles, an initial shift multiplier of 0.7 is assumed in the first cycle. If the refinement proves to be unstable, this starting value can be reset using the first DAMP parameter. In addition to this optimization of the CGLS shift multiplication factor, the individual parameter shifts are monitored each L. S. or CGLS cycle, and the shift multiplication factors are reduced (to a value between 0.5 and 1) for parameters that tend to oscillate. This applies only to refinements in which BLOC is not used. This produces an additional improvement in the convergence of the least-squares refinement, but (unlike Marquardt damping) has no effect on esds. CHIV V0 s0.1 atomnames The chiral volumes of the named atoms are restrained to the value V (in Aringsup3) with standard deviation s. The chiral volume is defined as the volume of the tetrahedron formed by the three bonds to each named atom, which must be bonded to three and only three non-hydrogen atoms in the connectivity list the (ASCII) alphabetical order of the atoms making these three bonds defines the sign of the chiral volume. Note that RTAB may be used to list chiral volumes defined in the same way but without restraining them. The chiral volume is positive for the alpha-carbon (CA) of an L-amino-acid if the usual names (N, CB and C) are used for the three non-hydrogen atoms bonded to it. It is also possible to define a chiral volume when two of these three atoms are chemically equivalent but have different names this may be useful to ensure that CB of a valine retains a pyramidal geometry with the conventional labeling of CG1 and CG2. Note that CHIV 0 (or just CHIV since the default V is zero) may be used to impose a planarity restraint on an atom which is bonded to three other non-hydrogen atoms, by making its chiral volume zero. CHIV restraints with zero and non-zero target values are listed separately in the restraints summary printed out after each refinement cycle. CONF atomnames maxd1.9 maxa170 The named atoms define a chain of at least four atoms. CONF generates a list of torsion angles with esds for all torsion angles defined by this chain for which the central bond is shorter than maxd and both the bond angles are less than maxa. CONF is often used to specify an n-membered ring, in which case the first three atoms must be named twice (n3 names in all). If no atoms are specified, all possible torsion angles not involving hydrogen are generated from the connectivity array. The torsion angles generated by CONF are also written to the. cif file if an ACTA instruction is present. All torsion angles follow the conventions defined by Allen amp Rogers, Acta Cryst. B25 (1969) 1326-1330. CONN bmax12 r atomnames or CONN bmax12 The CONN instruction fine-tunes the generation of the connectivity table and is particularly useful when pi-bonded ligands or metal ions are present in the structure. For the purposes of the connectivity table (which is always generated), bonds are all distances between non-hydrogen atoms less than r1 r2 0.5 Aring, where r1 and r2 are the covalent radii of the atoms in question (taking PART into consideration as explained below). A shell of symmetry equivalent atoms is also generated, so that all unique bonds are represented at least once in the list. Bonds, including those to symmetry equivalent atoms, may be deleted or added using the FREE or BIND instructions. Default values of r (identified by the scattering factor type) are stored in the program. These defaults may be changed (for both the connectivity table and the PLAN - n output) by using the full form of the SFAC instruction. Alternatively the defaults may be overridden for the named atoms by specifying r on a CONN instruction, in which case r is used in the generation of the connectivity list but not by the PLAN instruction. followed by an element name (the same as on a SFAC instruction) may also be employed on a CONN instruction (and also does not apply to PLAN ). The second form of the CONN instruction may be used to change the maximum coordination number bmax for all atoms (which defaults to 12 if there is no CONN instruction). If, after generating bonds as above and editing with FREE and BIND. there are more than bmax bonds to a given atom, the list is pruned so that only the bmax shortest are retained. A harmless side-effect of this pruning of the connectivity list is that symmetry operations may be stored and printed that are never actually used. Note that this option only removes one entry for a bond from the connectivity list, not both, except in the case of CONN 0 which ensures that there are no bonds to or from the named atoms. CONN 0 is frequently used to prevent the solvent water in macromolecular structures from making additional bonds to the macromolecule which confuse the generation of idealized hydrogen atoms etc. In some cases it will be necessary to use FREE to remove a bond from a light atom to an alkali metal atom (for example) in order to generate hydrogen atoms correctly. Refinements of macromolecules will often include BUMP and CONN 0 O200 gt LAST (where the water happens to begin with residue 200). LAST is used to indicate the last atom in the file, which saves trouble when adding extra waters. The CONN instruction, like ANIS and HFIX. must precede the atoms to which it is to be applied. Repeated CONN instructions are allowed the last relevant CONN preceding a particular atom is the one which is actually applied. CONN without atom names changes the default value of bmax for all following atoms. The following example illustrates the use of CONN: this would prevent bonds being generated from the iron atom to all 10 carbons in ferrocene. This also illustrates the calculation of the distances of the iron atom from the two ring planes. DAMP damp0.7 limse15 The DAMP parameters take different meanings for L. S. and CGLS refinements. For L. S.. damp is usually left at the default value unless there is severe correlation, e. g. when trying to refine a pseudo-centrosymmetric structure, or refining with few data per parameter (e. g. from powder data). A value in the range 1-10000 might then be appropriate. The diagonal elements of the least-squares matrix are multiplied by (1damp1000) before inversion this is a version of the Marquardt J. Soc. Ind. Appl. Math. 11 (1963) 431-441 algorithm. A side-effect of damping is that the standard deviations of poorly determined parameters will be artificially reduced it is recommended that a final least-squares cycle be performed with little or no damping in order to improve these estimated standard deviations. Theoretically, damping only serves to improve the convergence properties of the refinement, and can be gradually reduced as the refinement converges it should not influence the final parameter values. However in practice damping also deals effectively with rounding error problems in the (single-precision) least-squares matrix algebra, which can present problems when the number of parameters is large andor restraints are used (especially when the latter have small esds), and so it may not prove possible to lift the damping entirely even for a well converged refinement. Note the use of DAMP 0 0 to estimate esds but not apply shifts, e. g. when a final L. S. 1 job is performed after CGLS refinement. For CGLS refinements, damp is the multiplicative shift factor applied in the first cycle. In subsequent CGLS cycles it is modified based on the experience in the previous cycles. If a refinement proves unstable in the first cycle, damp should be reduced from its default value of 0.7. If the maximum shiftesd for a L. S. refinement (excluding the overall scale factor) is greater than limse, all the shifts are scaled down by the same numerical factor so that the maximum is equal to limse. If the maximum shiftesd is smaller than limse no action is taken. This helps to prevent excessive shifts in the early stages of refinement. limse is ignored in CGLS refinements. DANG d s0.04 atom pairs This instruction is interpreted in exactly the same way as DFIX. but the default value of s is twice the value of the first DEFS parameter (i. e. 0.04 if no DEFS instruction is used). The DFIX and DANG instructions appear separately in the table of restraint statistics. DANG is usually used for 1,3 or lsquoangle distancesrsquo, i. e. distances between two atoms that are both bonded to the same atom. The distance between the first and second named atom, the third and fourth, fifth and sixth etc. (if present) is restrained to a target value d with an estimated standard deviation s. d may refer to a free variable, otherwise it is considered to be fixed. Fixing d by adding 10 is not allowed, so the value may lie between 0 and 15. DEFS sd0.02 sf0.1 su0.01 ss0.04 maxsof1 DEFS may be used to change the default effective standard deviations for the following DFIX. SAME. SADI. CHIV. FLAT. DELU and SIMU restraints, and is useful when these are to be varied systematically to establish the optimum values for a large structure (e. g. using R free ). sd is the default for s in the SADI and DFIX instructions, and also for s1 and s2 in the SAME instruction. sf is the default effective standard deviation for CHIV and FLAT. su is the default for both s1 and s2 in DELU. and ss is the default s for SIMU. The default st for SIMU is set to twice the default s. maxsof is the maximum allowed value that an occupation factor can refine to occupation factors that are fixed or tied to free variables are not restricted. It is possible to change this parameter (to say 1.1 to allow for hydrogen atoms) when refining both occupation factors and Us for solvent water in proteins (a popular but suspect way of improving the R factor). DELU s10.01 s20.01 atomnames All bonds in the connectivity list connecting atoms on the same DELU instruction are subject to a rigid bond restraint, i. e. the components of the (anisotropic) displacement parameters in the direction of the bond are restrained to be equal within an effective standard deviation s1. The same type of restraint is applied to 1,3-distances as defined by the connectivity list (atoms 1, 2 and 3 must all be defined on the same DELU instruction). If s2 is omitted it is given the same value as s1. A zero value for s1 or s2 switches off the corresponding restraint. If no atoms are specified, all non-hydrogen atoms are assumed. DELU is ignored if (in the refinement cycle in question) one or both of the atoms concerned is isotropic in this case a hard restraint is inappropriate, but SIMU may be used in the usual way as a soft restraint. DELU without atom names applies to all non-hydrogen atoms. SFAC element names may also be referenced, preceded by the symbol . The default values of s1 and s2 may be changed by means of a preceding DEFS instruction. For many purposes DELU has been superseded by RIGU. DFIX d s0.02 atom pairs The distance between the first and second named atom, the third and fourth, fifth and sixth etc. (if present) is restrained to a target value d with an estimated standard deviation s. d may refer to a free variable, otherwise it is considered to be fixed. Fixing d by adding 10 is not allowed, so the value may lie between 0 and 15. If d is given a negative sign, the restraint is applied only if the current distance between the two atoms is LESS than d. This is an anti-bumping restraint, and may be used to prevent solvent (water) molecules from approaching too close to one another or to a macromolecule. Antibumping restraints may also be generated automatically using the BUMP instruction (see below). The default value of s is 0.02. The default s may be changed by means of a preceding DEFS instruction (see below). DISP E f fquot mu The DISP instruction allows the dispersion and (optionally) the absorption coefficient of a particular element (the name may be optionally prefaced by ) to be read in without having to use the full form of the SFAC instruction. It will typically be used for synchrotron data where the wavelength does not correspond to the values (for Ga, Cu, Mo and AgKalpha radiation) for which these terms are stored in the program. All other terms on the SFAC instruction are independent of the wavelength, so its short form may then be used. DISP instructions, if present, must come between the last SFAC and the UNIT instruction. The same isotropic or anisotropic displacement parameters are used for all the named atoms. The displacement parameters (and possibly free variable references) are taken from the first atom in the atom list that is linked to other atoms by EADP. The actual values, free variable references etc. given for the U ij of the other atoms are ignored. The atoms involved must either be all isotropic or all anisotropic. Opposite fluorines of PF 6 or disordered - CF 3 groups are good candidates for EADP, e. g. EADP applies an (exact) constraint . The SIMU instruction restrains the U ij components of neighboring atoms to be approximately equal with an appropriate (usually fairly large) esd. END is used to terminate an include file, and may also be included after HKLF in the . ins file. EQIV n symmetry operation Defines symmetry operation n for referencing symmetry equivalent atoms on any instruction which allows atom names, by appending n (where n is an integer between 1 and 511 inclusive) to the atom name. Such a symmetry operation must be defined before it is used it does not have to be an allowed operation of the space group, but the same notation is used as on the SYMM instruction. The same n may not appear on two separate EQIV instructions. Thus: could be used to calculate a torsion angle across a crystallographic twofold axis (note that this may be required because CONF with no atom names only generates torsion angles automatically that involve the unique atom list and a one atom deep shell of symmetry equivalents). If the instruction codeword refers to a residue, this is applied to the named atoms before any symmetry operation specified with n. Thus: would calculate the (hydrogen bond) distance between OG12 and (O23)3, i. e. between OG in residue 12 and the equivalent obtained by applying the symmetry operation defined by EQIV 3 to the atom O in residue 23. An extinction parameter x is refined, where F c is multiplied by: k 1 0.001 F c sup2lambdasup3 x sin(2theta) ndash14 where k is the overall scale factor. The wavelength dependence is needed for HKLF 2 (Laue) data. The program will print a warning if extinction (or SWAT ) may be worth refining, but it is not normally advisable to introduce it until all the non-hydrogen atoms have been found. For twinned and powder data, the F c sup2 value used in the above expression is based on the total calculated intensity summed over all components rather than the individual contributions, which would be easier to justify theoretically (but makes little difference in practice). For the analysis of variance and. fcf output file, the F o sup2 values are brought onto the absolute scale of F c sup2 by dividing them by the scale factor(s) and the extinction factor. The above expression for the extinction is empirical and represents a compromise to cover both primary and secondary extinction it has been shown to work well in practice but does not appear to correspond exactly to any of the expressions discussed in the literature. The article by Larson Crystallographic Computing (1970) 291-294 comes closest and should be consulted for further information. The same x, y and z parameters are used for all the named atoms. This is useful when atoms of different elements share the same site, e. g. in minerals, in which case EADP will probably be used as well. The coordinates and possible free variable references are taken from the EXYZ atom that comes first in the atom list. This must immediately follow the last atom of a FRAG fragment. FLAT s0.1 four or more atoms The named atoms are restrained to lie a common plane. This restraint is actually applied by restraining a sufficient number of tetrahedra involving the atoms in question to have (chiral) volumes of zero, using the same algorithm as CHIV. This way of applying a planarity restraint has good convergence properties because it does not fix the orientation of the plane in its current position. s should be given in Aringsup3 as for CHIV. but for comparison with other methods the r. m.s. deviation from the plane is also printed. The default values of s is set by the second DEFS parameter. FMAP code2 axis nl53 The unique unit of the cell for performing the Fourier calculation is set up automatically unless specified by the user using FMAP and GRID the value of axis must be non-zero to suppress the automatic selection. The program chooses a 53 x 53 x nl or 103 x 103 x nl grid depending on the resolution of the data. axis is 1, 2 or 3 to define the direction perpendicular to the layers. Dispersion corrections are applied (so that the resulting electron density is real) and Friedel opposites are merged after the least-squares refinement and analysis of variance but before calculating the Fourier synthesis. Reflections with sigma(F) relatively large compared with Fc are weighted down, this helps to reduce noise. The r. m.s. fluctuation of the map relative to the mean density is also calculated in the case of a difference map this gives an estimate of the noise level and so may be used to decide whether individual peaks are significant. Usually FMAP 2 is employed to find missing atoms, but if a significant part of the structure is missing, FMAP 5 or 6 may be better. ACTA requires FMAP 2 so that the difference density is on an absolute scale. If code is made negative, both positive and negative peaks are listed, sorted on the absolute value of the peak height. This is useful for neutron diffraction data. code2: Difference electron density synthesis with coefficients (F o ndashF c ) and phases phi(calc). code3: Electron density synthesis with coefficients F o and phases phi(calc). code4: Electron density synthesis with coefficients (2F o ndashF c ) and phases phi(calc). F(000) is included in the Fourier summations for code3 and 4. code5: Sim-weighted (2mF o - DF c ) Fourier. code6: Sim-weighted (2mF o - DF c ) Fourier, coefficients sharpened by multiplying with radic(EF). FRAG code17 a1 b1 c1 alpha90 beta90 gamma90 Enables a fragment to be input using a cell and coordinates taken from the literature. Orthogonal coordinates may also be input in this way. Such a fragment may be fitted to the set of atoms following an AFIX instruction with mcode (code must be greater than 16) there must be the same number of atoms in this set as there are following FRAG, and they must be in the same order. Atoms with zero coordinates are not fitted, but new coordinates are generated for these atoms. The atom names, sfac numbers, sof and U ij of the FRAG fragment are ignored, only the coordinates are used. A FRAG fragment may be given anywhere between UNIT and HKLF or END or in an include file, and must be terminated by a FEND instruction, but must precede any AFIX instruction which refers to it. This rigid fit is often a preliminary to a rigid group refinement (AFIX 6). FREE atom1 atom2 The specified bond is deleted from the connectivity list (if present). Only one of the two atoms may be an equivalent atom (i. e. have the extension n). FVAR osf1 free variables The overall scale factor is followed by the values of the free variables fv 2. For historical reasons, the overall scale factor is given throughout as the square root of the scale factor which multiplies F c sup2 in the least-squares refinement. SHELXL goes to some trouble to ensure that the initial value of the scale factor has very little influence. Firstly, if the initial scale is exactly 1.0, a quick structure factor summation with a small fraction of the total number of reflections is performed to estimate a new scale factor. If the values differ substantially then the new value is used. Secondly the scale factor is factored out of the least-squares algebra so that, although it is still refined, the only influence the previous value has is an indirect one via the weighting scheme and extinction correction. Before calculating electron density maps and the analysis of variance, and writing the structure factor file ( name. fcf ), the observed Fsup2 values and sigma(F o sup2) are brought onto an absolute scale by dividing by the squared scale factor. The free variables allow extra constraints to be applied to the atoms, e. g. for common site occupation factors or isotropic displacement parameters, and may be used in conjunction with the SUMP. DFIX and CHIV restraints. If there is more than one FVAR instruction, they are concatenated they may appear anywhere between UNIT and HKLF (or END ). GRID sl sa sd dl da dd Fourier grid, when not set automatically. Starting points and increments multiplied by 100. s means starting value, d increment, l is the direction perpendicular to the layers, a is across the paper from left to right, and d is down the paper from top to bottom. sl and dl need not be integral. A 103 x 103 x nl grid is only available when it is set automatically by the program. It is almost always better to let the program define this grid. HFIX mn U d atomnames HFIX generates AFIX instructions and dummy hydrogen atoms bonded to the named atoms, the AFIX parameters being as specified on the HFIX instruction. This is exactly equivalent to the corresponding editing of the atom list. The atom names may reference residues (by appending n to the name, where n is the residue number), or SFAC names (preceded by a sign). U may be any legal value for the isotropic temperature factor, e. g. 21 to tie a group of hydrogen U value to free variable 2, or -1.5 to fix U at 1.5 times U eq of the preceding normal atom. HFIX must come before the atoms to which it is to be applied. If more than one HFIX instruction references a given atom, only the first is applied. HFIX 0 is legal, and may be used to switch off following HFIX instructions for a given atom (which can be useful if they involve or a global reference to a residue class). HKLF N0 S1 r11. r331 0 0 0 1 0 0 0 1 sm1 m0 N defines the format of the data in the. hkl file, the scale factor S multiplies both F o sup2 and sigma(F o sup2) (or F o and sigma(F o ) for N 1 or 3) and the indices are transformed using the 3x3 matrix r 11. r 33. so that the new h is r 11 h r 12 k r 13 l etc. The matrix must have a positive determinant. It is essential that the cell, symmetry and atom coordinates in the . ins file correspond to the indices after transformation using this matrix. N is negative if reflection data follow in the same. ins file (deprecated), otherwise they are read from the . hkl file. The data are read in FORMAT(3I4,2F8.2,I4) (except for Nlt3) subject to Fortran conventions. They are terminated by a blank line or record with h, k and l all zero (except N1, which contains a terminator and a checksum). In the reflection formats given below, BN is the batch (or twin component) number if it is zero or absent, it is reset to one. sm multiplies all sigma-values and m is an integer offset needed to read condensed data (HKLF 1) both are included for compatibility with SHELX-76. Negative N is also only retained for historical reasons it is much better to keep the reflection data in the name. hkl file, otherwise the data can easily get lost when editing name. res to name. ins for the next job. N1: SHELX-76 condensed data, extremely compact but lossy and deprecated. N2: h k l F o sup2sigma(F o sup2) BN1 lambda in FORMAT(3I4,2F8.2,I4,F8.4) for refinement based on singlet Laue reflections. The data are assumed to be scaled for source intensity distribution and geometric factors and (if necessary) corrected for absorption. If lambda is zero or absent the value from the CELL instruction is used. N2 switches off the merging of equivalent reflections before refinement (i. e. sets MERG 0). Equivalents with different wavelengths are merged after refinement and the subsequent application of a dispersion correction, but before Fourier calculations. The remaining options (Ngt2) all require Fortran FORMAT(3I4,2F8.2,I4) other compatible formats (e. g. F8.0 or even I8) may be used. N3: h k l F o sigma(F o ) BN1 (if BN is absent or zero it is set to 1). The use of data corresponding to this format is allowed but is not recommended, since the generation of F o and sigma(F o ) from F o sup2 and sigma(F o sup2) is a tricky statistical problem and could introduce bias. N4: h k l F o sup2 sigma(F o sup2) BN1 is the standard reflection data file. Since F o sup2 is obtained as the difference of the experimental peak and background, it may be positive or slightly negative. BN may be made negative (e. g. by the Bruker program XPREP) to flag a reflection for inclusion in the Rfree reference set (see CGLS and L. S. with a second parameter of -1). N5: h k l F o sup2 sigma(F o sup2) m where m is the twin component number. Each measured F o sup2 value is fitted to the sum of k m F cm sup2 over all contributing components, multiplied by the overall scale factor. m should be positive for the last contributing component and negative for the remaining ones (if any). The values of F o sup2 and sigma(F o sup2) are taken from the last (prime) reflection in a group, and may simply be set equal for each component, but the indices h, k,l will in general take on different values for each component. The starting values of the twin factors k 2. k max(m) are specified on BASF instruction(s) k1 is given by one minus the sum of the other twin factors. Note that many simple forms of twinning can also be handled with HKLF 4 and a TWIN instruction to generate the indices of the remaining twin component(s) HKLF 5 is required if the reciprocal space lattices of the components cannot be superimposed exactly. HKLF 5 sets MERG 0, and may not be used with TWIN. N6: h k l F o sup2 sigma(F o sup2) m is used to input an indexed powder diffraction pattern. As for N5, there may be one or more sets of reflection indices corresponding to a single F o sup2 value. The last reflection in a group has a positive m value and the previous members of the group have negative m. The values of F o sup2 and sigma(F o sup2) are taken from the last (prime) reflection in a group, and may simply be set to the same values for the others. In contrast to N5, m is here the reflection multiplicity, and is defined as the number of equivalent permutations of the given h, k and l values, not counting Friedel opposites. This is intended for fitting resolved powder data for high symmetry crystal systems. For example, in a powder diagram of a crystal in the higher cubic Laue group (m-3m) the reflections 3 0 0 (which has multiplicity 3) and 2 2 1 (multiplicity 12) would contribute to the same measured F o sup2. HKLF 6 sets MERG 0 and may not be used with BASF or TWIN. There may be only one HKLF instruction and it must come last, except when HKLF - N is followed by reflection data, in which case the file is terminated by the end of the data. The HTAB instruction provides an analysis of the hydrogen bonds. A search is made for all hydrogen bonds for which HbullbullbullA lt r(A)dh and angDHA gt 110ordm. If it appears likely that the hydrogens have been assigned wrongly (e. g. two - OH groups have been assigned to the same ObullbullbullO vector) a suitable warning message appears. This output should be checked carefully, since the algorithms used by HFIX AFIX to place hydrogens are by no means infallible To obtain esds on the distances and angles involved in the hydrogen bond, the second form of the HTAB instruction (and if necessary EQIV ) should be used (see below) HTAB without atom names is used first to find the necessary symmetry transformations for EQIV and writes the appropriate HTAB (with atom names) and EQIV instructions to the end of the. res file. This can be re-input by moving the HKLF and END instructions in the. res file to after the new HTAB instructions and renaming the file as. ins . When doing this, care should be taken not to change or delete any existing EQIV instructions. Non-classical C9472HbullbullbullO hydrogen bonds are generated and should be checked carefully since they may be controversial HTAB donor-atom acceptor-atom The second form of the HTAB instruction is required to generate the esds and the CIF output records. The donor atom D and acceptor A should be specified the program decides which of the hydrogen atoms (if any) makes the most suitable hydrogen bond linking them. Only the acceptor atom may specify a symmetry operation (n) because CIF requires this. ISOR s0.1 st0.2 atomnames The named atoms are restrained with effective standard deviation s so that their U ij components approximate to isotropic behavior however the corresponding isotropic U is free to vary. ISOR is useful for water molecules for which RIGU. DELU and SIMU are inappropriate. ISOR should in general be applied as a weak restraint, i. e. with relatively large sigmas, for the reasons discussed above (see SIMU ) however it is also useful for preventing individual atoms from becoming non-positive-definite (NPD). However it should not be used indiscriminately for this purpose without investigating whether there are reasons (e. g. disorder, wrong scattering factor type etc.) for the atom going NPD. If (according to the connectivity table, i. e. ignoring attached hydrogens) the atom is terminal (or makes no bonds), st is used instead as the esd. If s but not st is specified, st is set to twice s. If no atoms are given, all non-hydrogen atoms are understood. SFAC element names may also be referenced, preceded by . s or st may be set to zero to switch off the appropriate restraints. ISOR without atom names (or ISOR if residues are used) applies this restraint to all non-hydrogen atoms. Note also the use of the keyword LAST to indicate the last atom in the. ins file an anisotropic refinement of a macromolecule will often include: assuming that the solvent water starts with O201 and continues until the end of the atom list. ISOR should in general be given a much larger esd (and hence lower weight) than DELU or RIGU whereas there is good evidence that DELU and RIGU restraints should hold accurately for most covalently bonded systems, ISOR (and SIMU ) are only rough approximations to reality. Lattice type: 1P, 2I, 3rhombohedral obverse on hexagonal axes, 4F, 5A, 6B, 7C. N must be made negative if the structure is non-centrosymmetric. Wavelength-dependent values of f, fquot and optionally mu may be defined for an element E by means of the LAUE instruction, which is used in conjunction with the HKLF 2 reflection data format in which the wavelength is given separately for each reflection. This is primarily intended for refinement of structures against Laue data collected using synchrotron radiation. There is no provision for handling overlapping reflection orders, scaling for the source intensity distribution, Lp and absorption corrections. A dummy wavelength (e. g. 1.0) should be given on the CELL instruction and the absorption coefficient output by the program should be ignored. The element symbol may be preceded by but this is optional. The line immediately following the LAUE instruction is always ignored, and so may be used for headings. The following lines contain values of wavelength (in Aring), f and fquot in Fortran FORMAT(F7.3,2F8.3) further information may follow on the same line but will be ignored. The wavelength values must be in ascending order and will be linearly interpolated the wavelength intervals do not need to be equal (but it is more efficient if most of them are) and should indeed be smaller in the region of an absorption edge. This list is terminated by a blank line. There should only be one LAUE instruction for each element type if a reflection wavelength is outside the range specified, the constant f and fquot values defined by the corresponding SFAC instruction are used instead. A LAUE instruction must be preceded by (normal) SFAC and UNIT instructions referencing the elements in question, and by all atoms. Thus the LAUE instruction(s) are usually the last instructions before HKLF 2 (or -2) at the end of the . ins file (which facilitates editing). The filename construction may conveniently be used to read long LAUE tables from include files without echoing them. Write reflection lists to the. fcf file. Only one LIST instruction is allowed. m1 . List h, k,l, F o. F c and phase (in degrees) in X-PLOR format. Only unique reflections after removing systematic absences, scaling to an absolute scale of F(calc), applying dispersion and extinction or SWAT corrections (if any), and merging equivalents including Friedel opposites are included. If F o 2 was negative, F o is set to zero. Reflections suppressed by OMIT or SHEL or reserved for R(free) are not included. m2 . List h, k,l, F o. sigma(F o ) and phase angle in degrees in Fortran FORMAT(3I4,2F8.2,I4) for the reflection list as defined for m1. m3 . List h, k,l, F o. sigma(F o ), A(real) and B(imag) in Fortran FORMAT(3I4,4F8.2), the reflections being processed exactly as for m2. m4 . List h, k,l, F c sup2, F o sup2, sigma(F o sup2) and a one-character status flag. F o sup2 are scaled to F c sup2 and possibly corrected for extinction, but no corrections have been made for dispersion and no further merging has been performed. Fortran FORMAT(3I4,2F12.2,F10.2,1X, A1) is employed. The status flag is o (observed), x observed but suppressed using OMIT h k l, SHEL or reserved for R(free), or lt (F o sup2 is less than t. s(F o sup2), where t is one half of the F-threshold s specified on an OMIT instruction). m5 . Write h, k,l, F o. F c. and f (phase angle in degrees) in FORMAT(3I4,2F10.2,F7.2) for the reflection list as defined for m1. Like the m1 option, this is intended for input to some standard macromolecular FFT programs ( such as W. Fureys PHASES program), thereby providing a possible route to a graphical display of the electron density. m6 . Write h, k,l, F o sup2, sigma(F o sup2), F c and phi(phase angle in degrees) for the reflection list as defined for m1. This is the format required for input to shelXle or Coot. m7 . List h, k,l, F o sup2, sigma(F o sup2) followed on the same line by F c sup2 for each twin component (-1 if a twin component makes no contribution to the reflection). m8 . List h, k,l, F o sup2, sigma(F o sup2), F c sup2, phi(phase angle in degrees), d-spacing in Aring and 1radicw where w is the weight derived from the weighting scheme (WGHT ) and used in the refinement. For weak reflections 1radicw should be only a little larger than sigma (F o sup2). This list is on an absolute scale and is detwinned, merged (according to the point group of the crystal) and sorted, but without eliminating the anomalous contributions (except in the calculation of phi, so the corresponding electron density is real. For m4 only, mult is a constant multiplicative factor applied to all the quantities output (except the reflection indices), and may be used if there are scaling problems. For other m options mult is ignored. For m2,3 or 4 only, a blank line is output at the end of the file as a terminator. The reflection list is written to the file name. fcf . which is in CIF format for m3,4,6 or 8. m4 was the standard archive format for small-molecule structures, and m 6 for macro-molecules. However now that all the IUCr journals and many others accept the new CIF format that contains embedded. res and. hkl files, the. cif file should be preferred for archiving the structure. This has the dvantage that the refinement can be repeated exactly (after extracting the files with SHREDCIF) and that it can be used with all HKLF data formats. And there are no problems with reflections flagged for use in the free R-factor. L. S. nls0 nrf0 nextra0 nls cycles of full-matrix least-squares refinement are performed, followed by a structure factor calculation. When L. S. (or CGLS ) is combined with BLOC. each cycle involves refinement of a block of parameters which may be set up differently in different cycles. If no L. S. or CGLS instruction is given, L. S. 0 is assumed, i. e. structure factors are still calculated. If nrf is positive, it is the number of these cycles that should be performed before applying ANIS. This two-stage refinement is particularly suitable for the early stages of least-squares refinement experience indicates that it is not advisable to let everything go at once Negative nrf indicates which reflections should be ignored during the refinement but used instead for the calculation of free R-factors in the final structure factor summation for example L. S. 4 ndash10 would ignore every 10th reflection for refinement purposes. However the recommended value is -1, to use the R free set defined in the. hkl file, which is independent of the space group and the MERG. OMIT and SHEL settings. R free Brunger, Nature 355 (1992) 472-475 provides a check as to whether the structure is being over-refined. To avoid bias, the R free reflections are not used for Fourier calculations in SHELXL and are also not included in the LIST 6 output that can be used to make a map with the program Coot. nextra is the number of additional parameters that were derived from the data when squeezing the structure etc. It ensures that the standard deviations and GooF are estimated correctly they would be underestimated if the number of extra parameters is not specified. nextra should be left at the default of zero except when squeeze has been used. If n is equal to 2 the reflections are sorted and merged before refinement, but if the structure is non-centrosymmetric the Friedel opposites are not combined before refinement. If n is 1 the indices are converted to a standard setting in which l is maximized first, followed by k, and then h if n is zero, the data are neither sorted nor converted to a standard setting. n3 is the same as n2 except that Friedel opposites are also merged this introduces small systematic errors for non-centrosymmetric structures and should only be used for good reason. Note that the reflections are always merged, and Friedel opposites combined, before performing Fourier calculations so that the (difference) electron density is real and correctly scaled. Even with n0 the program may change the reflection order within each data block to optimize the vectorization of the structure factor calculations. Note that MERG may not be used in conjunction with HKLF 5 or 6. MERG 2 is now the standard for small molecules and is required for the production of CIF files. MERG 4 averages all equivalents including Friedel opposites, and in contrast to MERG 3 also sets all fquot values to zero it is often used in refinement of macromolecules. MORE sets the amount of (printer) output m takes a value in the range 0 (least) to 3 (most verbose). MORE 0 also suppresses the echoing to the . lst file of any instructions or atoms which follow it (until the next MORE instruction). If m is negative, lists of parameters and the full covariance matrix are written to the. mat file. MOVE dx0 dy0 dz0 sign1 The coordinates of the atoms that follow this instruction are changed to: xdxsignx, ydysigny, zdzsignz until superseded by a further MOVE. MOVE should not be used at the same time as the specification of zero coordinates to indicate that an atom should not be used in fitting a fragment of known geometry (e. g. AFIX 66), because after the move the coordinates will no longer be zero MPLA na atomnames A least-squares plane is calculated through the first na of the named atoms, and the equation of the plane and the deviations of all the named atoms from the plane are listed with estimated standard deviations (from the full covariance matrix). The angle to the previous least-squares plane (if any) is also calculated, but some approximations are involved in estimating its esd. na must be at least 3. If na is omitted the plane is fitted to all the atoms specified. NCSY DN sd0.1 su0.05 atoms The NCSY instruction applies local non-crystallographic symmetry restraints. In contrast to global NCS constraints, these do not save CPU time but do not require the definition (and refinement) of a matrix transformation and mask. They are very flexible, and can accommodate rotation of domains relative to each other etc. Since for macromolecules at modest resolution the 1,2-and 1,3-distances are normally restrained to fixed target values by DFIX and DANG. the NCS restraints are generated for equivalent 1,4-distances (if sd is non zero or absent) and equivalent isotropic U-values (if su is non-zero or absent). The default sd is set to five times the first DEFS parameter, and the default su is equal to the fourth DEFS parameter. For each atom the program attempts to find a corresponding atom with the same name but with a residue number DN greater than the residue number of the named atom. If sd is greater than zero, the connectivity array is used to find 1,4-distances for which both atoms are specified in the same NCSY instruction a SADI restraint is then created to make the distance equivalent to the same distance between the equivalent atoms. This is not quite the same as restraining torsion angles to be the same, because and ndash gauche rotamers would have the same distance however it is chemically plausible that equivalent side-chain conformations could differ in this way. If su is greater than zero (or absent), a SIMU restraint is generated to make the U-values approximately equal for each pair of lsquoequivalentrsquo atoms, provided that both are isotropic. NCS restraints should be used whenever possible for isotropic (protein) refinement at modest resolution, since they increase the effective data to parameter ratio and so have a similar effect to that of increasing the resolution of the data. For example, to apply three-fold NCS restraints to a protein structure containing three equivalent chains numbered 1001-1109, 2001-2109 and 3001-3109, the following two instructions are all that is required: These atom lists may easily be modified to leave out particular loops, residues or side-chains. This is not only easier than specifying a transformation matrix and mask: it also will correspond more closely to reality, because the restraints are more flexible than constraints and also act locally rather than globally. The NEUT instruction takes no parameters and is designed to facilitate refinement against neutron diffraction data. If present, it should normally appear just before the first SFAC instructions. It has three effects: 1. The special treatment of H and D atoms is switched off except for the generation and refinement of hydrogen atoms with HFIX and AFIX. AFIX 87 and 137 take the negative scattering length of H into account when interpreting the circular difference density map. 2. If NEUT comes before a SFAC instruction that contains atom names but not numbers, neutron scattering lengths and absorption coefficients are used for those elements. Except for D that is assumed to be a pure isotope, the scattering lengths are the weighted mean values for natural isotopic abundances. The neutron data are taken from the ILL Neutron Data Booklet, Dianoux, A.-J. Lander, G. second edition (2003). DISP can be added as required, e. g. for cadmium. The full form of the SFAC instruction may still be used to input mean scattering lengths for non-natural isotopic mixtures, or for atomic numbers greater than 94. 3. If the isotropic U of an atom (usually H or D) is given a value - k where -0.5 gt - k gt -5.0, it is set to k times the U-value of the last normal atom, but in contrast to the similar action when NEUT is not set, both atoms contribute to the calculation of the derivatives used in the least-squares calculations, so both atoms must be isotropic. This significantly reduces the number of degrees of freedom of the refinement and so would be expected to reduce the gap between R1 free and R1 for a macromolecule, especially when the number of neutron data is limited. A relatively large k value (say 2.5) appears to be appropriate for D 2 O and H 2 O molecules when refining against neutron data. The named atoms are retained in the atom list but ignored in the structure factor calculation and least-squares refinement. This instruction may be used, together with L. S. 0 and FMAP 2, to create an omit map to get a clearer picture of disordered regions of the structure this concept will be familiar to macromolecular crystallographers. In particular, OMIT H can be used to check the hydrogen atom assignment of - OH groups etc. If an actual peak is present within 0.31 Aring of the calculated hydrogen atom position, the electron density appears in the Peak column of the output created by PLAN with a negative first parameter. OMIT H must be used for this if residues are employed. OMIT s-2 2theta(lim)180 If s is given as zero or negative, all reflections with F o sup2 lt 0.5ssigma(F o sup2) are replaced by 0.5ssigma(F o sup2) thus if no OMIT instruction is given the default action is to replace all F o sup2 values less than - sigma(F o sup2) by - sigma(F o sup2). If s is positive it is interpreted as a threshold for flagging reflections as unobserved. Unobserved data are not used for least-squares refinement or Fourier calculations, but are retained for the calculation of R-indices based on all data, and may also appear (flagged with an asterisk) in the list of reflections for which F o sup2 and F c sup2 disagree significantly. Internally in the program s is halved and applied to F o sup2, so for positive F o sup2 the test is roughly equivalent to suppressing all reflections with F o lt ssigma(F o ). Note that s may be set to 0 or (as in the default setting) to a negative threshold (to modify very negative F o sup2). An OMIT instruction with a positive s value is not allowed in combination with ACTA. because it may introduce a bias in the final refined parameters individual aberrant reflections may still be suppressed using OMIT h k l, even when ACTA is used. 2theta(lim) defines a limiting 2theta above which reflections are totally ignored they are rejected immediately on reading in. The SHEL command may also be used to ignore reflections above or below particular limiting resolution values. The reflection h, k,l (the indices refer to the standard setting after data reduction, and correspond to those in the list of lsquodisagreeable reflectionsrsquo after refinement) is ignored completely. Since there may be perfectly justified reasons for ignoring individual reflections (e. g. when a reflection is truncated by the beam stop) this form of OMIT is allowed with ACTA however it should not be used indiscriminately. If MERG N with non-zero N is employed (or the (default) MERG 2 is assumed), all reflections that would generate the final indices h, k,l are ignored. It is best to use the indices exactly as given in the table of the most disagreeable reflections in the . lst file it may be necessary to omit both members of a Friedel pair. The following atoms belong to PART n of a disordered group. The automatic bond generation ignores bonds between atoms with different PART numbers, unless one of them is zero (the default value until a PART instruction is read). If a site occupation factor (sof) is specified on the PART instruction, it overrides the value on the following atom instructions (even if set via an AFIX instruction) until a further PART instruction, e. g. PART 0, is encountered). If n is negative, the generation of special position constraints is suppressed and bonds to symmetry generated atoms with the same or a different non-zero PART number are excluded this is suitable for a solvent molecule disordered on a special position of higher symmetry than the molecule can take (e. g. a toluene molecule on an inversion center). A PART instruction remains in force until a further PART instruction is read PART 0 should be used to continue with the non-disordered part of the structure. Some care is necessary in generating hydrogen atoms where disordered groups are involved. If the hydrogen atoms are assigned a PART number, then even if the atom to which they are attached has no part number (i. e. PART 0) the above rules may be used by the program to work out the correct connectivity for calculating the hydrogen atom positions. HFIX hydrogens are assigned the PART number of the atom to which they are attached. If the hydrogens and the atom to which they are attached belong to PART zero but the latter is bonded to atoms with non-zero PART, the lowest of these non-zero PART numbers is assumed to be the major component and is used to calculate the hydrogen positions. In general, if the same residue numbers and names and the same atom names but different PART numbers are used for different disorder components in a macromolecule, HFIX will generate hydrogen atoms correctly without any special action being required, so it is recommended that the hydrogen atoms should be introduced with HFIX after the disorder has been fully accounted for. For example the use of HFIX with the following disordered serine residue: would set up the AFIX hydrogens as if the following had been input. Note that only one, fully occupied, hydrogen is attached to CA for this reason, and also to prevent small inconsistencies in the DFIX and DANG restraints, the disorder should be traced back one more atom than can be resolved (i. e. CB should be split even if it does not look as though this would be necessary in an electron density map): where free variable 2 is the occupation factor for PART 1 (say 0.7) and the occupation factor of the second component is tied to 1-fv(2) (i. e. 0.3). The value for this free variable is set on the FVAR instruction and is free to refine. If there were more than two components, a linear free variable restraint (SUMP ) could be used to restrain the sum of occupation factors to unity. PLAN npeaks20 d1 d2 If npeaks is positive a Fourier peak list is printed and written to the . res file if it is negative molecule assembly and line printer plots are also performed (this option is clearly only of historical interest). Distances involving peaks which are less than r1r2d1 (the covalent radii r are defined via SFAC 1 and 2 refer to the two atoms concerned) are printed and used to define molecules for the line printer plots. Distances involving atoms andor peaks which are less than r1r2d2 are considered to be non-bonded interactions however distances in which both atoms are hydrogen or at least one is carbon (recognised by SFAC label C) are ignored. These non-bonded interactions are ignored when defining molecules, but the corresponding atoms and distances are included in the. lst file. Thus an atom or peak may appear in more than one map, or more than once on the same map. A table of the appropriate coordinates and symmetry transformations appears at the end of each molecule. Negative d2 includes hydrogen atoms in the line printer plots, otherwise they are left out (but included in the distance tables). For the purposes of the PLAN instruction, a hydrogen atom is one with a radius of less than 0.4 Aring. Peaks are assigned the radius of SFAC type 1, which is usually set to carbon. Peaks appear on the printout as numbers, but in the. res file they are given names beginning with Q and followed by the same numbers. Peak heights are also written to the. res file (after the sof and dummy U values) in electrons Aring ndash3. A default npeaks of 20 is set by FMAP to obtain line printer plots, an explicit PLAN instruction with negative npeaks is required. If npeaks is positive the nearest unique atoms to each peak are tabulated, together with the corresponding distances. A table of shortest distances between peaks is also produced. If npeaks is positive d1 and d2 have a different meaning. The default of d1 is then -1 and causes the full peaklist to appear in the. res file. If it is positive (say 2.3) then the full peaklist is still printed in the . lst file, but only suitable candidates for (full occupancy) water molecules appear in the . res file (with SFAC 4 and U set to 0.75). These water molecules must be less than 4 Aring from an atom which begins with O, N or W, and may not be nearer than d2 (default 3.0) from any atom which does not begin with O, N, W or H, and may not be nearer than d1 to any O, N or W atom or to other potential waters which have larger peak heights. This facility is intended for extending the water structure of proteins in connection with BUMP and SWAT. To include the waters in the next refinement job, their names need to be changed and they need to be moved to before the HKLF instruction at the end of the atom list in the new. ins file. The heights and positions of the highest (difference) electron density maximum and the deepest minimum are output irrespective of the PLAN parameters. This sets the parameter p used in the weighting scheme for the RIGU restraint Thorn, Dittrich amp Sheldrick, Acta Cryst. A 68 (2012) 448-451. It will very rarely be necessary to change p from its default value. Followed by a comment on the same line. This comment is copied to the . res file. A line beginning with at least one blank may also be used as a comment, but such comments are only copied to the . res file if the line is completely blank REM comments are always copied. Comments may also be included on the same line in any instruction following the character . RESI class number0 alias Until the next RESI instruction, all atoms are considered to be in the specified residue, which may be defined by a class (up to four characters, beginning with a letter) or number (up to four digits) or both. The same atom names may be employed in different residues, enabling them to be referenced globally or selectively. Residues of the same class may have different residue numbers but each number must always have the same class. Residues may be referenced by any instruction that allows atom names the reference takes the form of the character followed by either the residue class or number without intervening spaces. If an instruction codeword is followed immediately by a residue number, all atom names referred to in the instruction are assumed to belong to that residue unless they are themselves immediately followed by and a residue number, which is then used instead. Thus: would cause the calculation of an angle N4 - H04 - O11, where the first two atoms are in residue 4 and the third is in residue 11. If the instruction codeword is followed immediately by a residue class, the instruction is effectively duplicated for all residues of that class. may be used to duplicate the instruction for all residues this includes the default class (residue number 0) which applies until the first RESI instruction is encountered. Thus: would calculate least-squares planes through atoms CB to CZ inclusive of all residues of class Phe (phenylalanine). In the special case of HFIX. only the first instruction which applies to a given atom is applied. Thus: would add hydrogens to the N-terminal nitrogen (residue 1) of a protein to generate a (protonated) - NH 3 group, but all other (amide) nitrogens would become - NH-. Individual atom names in an instruction may be followed by and a residue number, but not by or and a residue class. If an atom name is not followed by a residue number, the current residue is assumed (unless overridden by a global residue number or class appended to the instruction codeword). The symbols meaning the next residue and - meaning the preceding residue(i. e. residues number n1 and n-1 if the current residue number is n) may be appended to atom names but not to instruction codenames. Thus the instruction: could be used to calculate all the peptide omega torsion angles in a protein or polypeptide. If (as at the C-terminus in this example) some or all of the named atoms cannot be found for a particular residue, the instruction is simply ignored for that residue. n does not refer to a residue it uses the symmetry operation n defined by a preceding EQIV n instruction to generate an equivalent of the named atom (see EQIV ). alias specifies an alternative value of the residue number so that cyclic chains of residues may be created for a cyclic pentapeptide (residue numbers 2,3. 6) it could be set to 1 for residue 6 and to 7 for residue 2. If more than one RESI instruction refers to the same number, alias only needs to be specified once. alias is referenced only by the and - operations (see above), and a value used for alias may not be used as a residue number on a RESI instruction. Note that if there is more than one cyclic peptide in the asymmetric unit, it is a good idea to leave a gap of at least two residue numbers between them, so a cyclic pentapeptide with two molecules in the asymmetric unit could be numbered 2 to 6 and 9 to 13, with aliases 7 on RESI 2, 1 on RESI 6, 14 on RESI 9 and 8 on RESI 13. It will generally be found convenient for applying restraints etc. to use the same names for atoms in identical residues. Since SHELXL does not recognize chain IDrsquos (used in PDB format) it is normal to add a constant to the residue numbers to denote a chain (e. g. chain A could be 1001 to 1234 and chain B 2001 to 2234). RIGU s10.004 s20.004 atomnames Apply enhanced rigid bond restraints with esds s1 for 1,2-distances and s2 for 1,3 Thorn, Dittrich amp Sheldrick, Acta Cryst. A 68 (2012) 448-451. This may be considered a hard restraint and so these low esds are appropriate and will rarely need changing. Often it will replace DELU. since it generates 3 or 6 restraints rather than 1 or 2, but in some cases it might be worth combining it with a DELU restraint that has a smaller esd. A zero value for s1 or s2 switches off the corresponding restraint. If no atoms are specified, all non-hydrogen atoms are assumed. RIGU is ignored if (in the refinement cycle in question) one or both of the atoms concerned is isotropic in this case a hard restraint is inappropriate, but SIMU may be used in the usual way as a soft restraint. RIGU without atom names applies to all non-hydrogen atoms. SFAC element names may also be referenced, preceded by the symbol . RTAB codename atomnames Chiral volumes (one atomname), bonds (two), angles (three) and torsion angles (four atomnames) are tabulated compactly against residue name and number. codename is used to identify the quantity being printed it must begin with a letter and not be longer than 4 characters (e. g. Psi or omeg). There may not be more than 4 atom names (except for D2CG). It is assumed that the atoms have the same names in all the required residues. For chiral volumes only, the necessary bonds must be present in the connectivity list, and the same sign conventions are employed as for CHIV. Since the atoms do not themselves have to be in the same residue (it is sufficient that the names match), the residue name (if any) is printed as that of the first named atom for distances, the second for angles, and the third in the case of torsion angles. The latter should be consistent with generally accepted conventions for proteins. If RTAB refers to more than one residue (e. g. RTAB), it is ignored for those residues in which not all the required atoms can be found (e. g. some of the main chain torsional angles for the terminal residue in a protein). If the codename is D2CG, the distance of the first atom to the unweighted centroid of the remaining atoms is calculated (with esd). This is useful for finding distances to mid-points of cyclopentadiene rings for example. SADI s0.02 pairs of atoms The distances between the first and second named atoms, the third and fourth, fifth and sixth etc. (if present) are restrained to be equal with an effective standard deviation s. The SAME and SADI restraints are analyzed together by the program to find redundant and implied restraints. The same effect as is obtained using SADI can also be produced by using DFIX with d tied to a free variable, but the latter costs one more least-squares parameter (but in turn produces a value and standard uncertainty for this parameter). The default effective standard deviations for SADI may be changed by means of a DEFS instruction before the instruction in question. A SADI instruction without any atom names causes SADI instructions that are equivalent to all the SAME instructions to be written to end of the. res file. This is useful if it is necessary to model a disorder involving atoms related by SAME. SAME s10.02 s20.04 atomnames The list of atoms (which may include the symbol gt meaning all intervening non-hydrogen atoms in a forward direction, or lt meaning all intervening non-hydrogen atoms in a backward direction) is compared with the same number of atoms which follow the SAME instruction. All bonds in the connectivity list for which both atoms are present in the SAME list are restrained to be the same length as those between the corresponding following atoms (with an effective standard deviation s1). The same applies to 1,3 distances (defined by two bonds in the connectivity list which share a common atom), with standard deviation s2. The default value of s1 is taken from the first DEFS parameter the default value of s2 is twice this. s1 or s2 may be set to zero to switch off the corresponding restraints. The program automatically sets up the n(n-1)2 restraint equations required when n interatomic distances should be equal. Only the minimum set of restraints needs to be specified in the. ins file redundant restraints are ignored by the program, provided that they have the same or larger sigma values as the unique set of restraints. See also SADI and NCSY for closely related restraints. The position of a SAME instruction in the input file is critical. SAME provides an elegant way of specifying that chemically identical but crystallographically independent molecules have the same 1,2 and 1,3 distances, e. g. etc. This requires just n-1 SAME instructions for n equivalent molecules. In a more complicated example, assume that a structure contains several toluene solvent molecules that have been assigned the same atom names (in the same order) and the same residue name (Tol) but different residue numbers, then one SAME instruction suffices: This instruction may be inserted anywhere except after the last Tol residue the program applies it as if it were inserted before the next atom that matches C1Tol. This is convenient for proteins with repeated non-standard residues, since one command suffices to apply suitable restraints, and no target values are needed. In this case it would also be reasonable to impose local two-fold symmetry for each phenyl ring, so a further SAME instruction could be added immediately before one toluene residue (the ring is assumed to be labeled cyclically C1. C6 followed by the methyl group C7 which is attached to C1): which is equivalent to: Note that these two SAME restraints are all that is required, however many Tol residues are present the program will generate all indirectly implied 1,2 and 1,3 equal-distance restraints In this case it would also be sensible to restrain the atoms of each toluene molecule to be coplanar by a FLAT restraint: SAMEXYZ, where XYZ is a residue name, now operates differently to SAMEN (where N is a residue number) or SAME without a residue number, both of which must be immediately followed by atoms in the same order as on the SAME instruction (H atoms are ignored). SAMEXYZ no longer uses the following atoms but is applied to all residues with the name XYZ, so the atoms must have the same names in the same order in each of these residues so that the program knows which are equivalent. For example, if we have six THF solvent molecules which should be restrained in this way, the THF molecules are preceded by RESI 1 THF, RESI 2 THF. RESI 6 THF and are each followed by RESI 0 (which can be omitted if another RESI instruction follows immediately). In this case the THF atoms should have the same names in the same order in each THF residue. Only two SAME instruction are required and may (now) appear anywhere in the. ins file: Hydrogen atoms can be added later with a single instruction: Alternately SAME1 O1 C4 and SAME1 O1 C4 2 O. SAMEWAT OW HW1 HW2 will not have any effect even if each water molecule is in a separate residue with the name WAT and atoms OW HW1 and HW2, but either: should work. These examples illustrate the way in which residues can be used to make the . ins file much simpler and easier to understand. Note however that because of a design limitation in PLATONCheckCIF, the number of characters in the atom name plus the number of characters in the residue number (plus two if ACTA TABS is set) should not be greater than 7. Element symbols which define the order of scattering factors to be employed by the program. The first 94 elements of the periodic system are recognized. The element name may be preceded by but this is not obligatory (the character is allowed for logical consistency but is ignored). The program uses the neutral atom scattering factors, f, fquot and absorption coefficients from International Tables for Crystallography, Volume C (1992), Ed. A. J.C. Wilson, Kluwer Academic Publishers, Dordrecht: Tables 6.1.1.4 (pp. 500-502), 4.2.6.8 (pp. 219-222) and 4.2.4.2 (pp. 193-199) respectively. The covalent radii stored in the program are based on experience rather than taken from a specific source, and are deliberately overestimated for elements which tend to have variable coordination numbers so that bonds are not missed, at the cost of generating the occasional non-bond. The default radii (not those set for individual atoms by CONN ) are printed before the connectivity table. SFAC E a1 b1 a2 b2 a3 b3 a4 b4 c f f mu r wt Scattering factor in the form of an exponential series, followed by real and imaginary dispersion terms, linear absorption coefficient, covalent radius and atomic weight. The element label E consists of up to 4 characters beginning with a letter (e. g. Ca2) and should be included before a1 for consistency the first label character may be a , but this is ignored (note however that the , if used, counts as one of the four characters, leaving only three for the rest of the label). The two SFAC formats may be used in the same . ins file the order of the SFAC instructions (and the order of element names in the first type of SFAC instruction) define the scattering factor numbers which are referenced by atom instructions. The units of mu should be barnsatom, as in Table 4.2.4.2 of International Tables, Volume C (see above). For neutrons either the NEUT instruction should come before an SFAC instruction that only contains atom names, or this format can be used, with a1. b4 set to zero. Hydrogen atoms are treated specially by SHELXL they are recognized by having the scattering factor number that corresponds to H or D on the SFAC instruction. This special treatment of H and D does not apply if NEUT is given before SFAC. SHEL lowresinfinite highres0 Reflections outside the specified resolution range in Aring are ignored completely. This instruction is often used for macromolecules. SIMU s0.04 st0.08 dmax2.0 atomnames Atoms closer than dmax are restrained with effective standard deviation s to have the same U ij components. If (according to the connectivity table, i. e. ignoring attached hydrogens) one or both of the two atoms involved is terminal (or not bonded at all), st is used instead as the esd. If s but not st is specified, st is set to twice s. If no atoms are given, all non-hydrogen atoms are understood. SIMU with no atoms applies to all non-hydrogen atoms in all residues. SFAC element names may also be referenced, preceded by . The interatomic distance for testing against dmax is calculated from the atom coordinates without using the connectivity table (though the latter is used for deciding if an atom is terminal or makes no bonds). Note that SIMU should in general be given a much larger esd (and hence lower weight) than RIGU and DELU whereas there is good evidence that RIGU and DELU restraints should hold accurately for most covalently bonded systems, SIMU (and ISOR ) are only rough approximations to reality. s or st may be set to zero to switch off the appropriate restraints. SIMU is based on the observation that the U ij values on neighboring atoms in larger molecules tend to be both similar and (when the resolution is poor) significantly correlated with one another. By applying a very weak restraint of this type, we allow a gradual increase and change in direction of the anisotropic displacement parameters as we go out along a side-chain, and we restrain the motion of atoms perpendicular to a planar group (which DELU and RIGU cannot influence). The use of a distance criterion directly rather than via the connectivity table enables the restraints to be applied automatically to partially overlapping disordered atoms, for which it is an excellent approach. dmax can be set so that coordination distances to metal ions etc. are excluded. Terminal atoms tend to show the largest deviations from equal U ij s and so st should be set higher than s (or made equal to zero to switch off the restraints altogether). SIMU restraints are NOT recommended for SMALL molecules and ions, especially if free rotation or torsion is possible (e. g. C 5 H 5 - groups, BF 4 ions). For larger molecular fragments, the effective rotation angles are smaller, and the assumption of equal U ij for neighboring atoms is more appropriate: both translation and libration of a large fragment will result in relatively similar U ij components on adjacent atoms. SIMU may be combined with ISOR. which applies a further soft but quite different restraint on the U ij components. SIMU may also be used when one or both of the atoms concerned is isotropic, in which case experience indicates that a larger esd (say 0.1 Aringsup2) is appropriate. The default value of s may be changed by a preceding DEFS instruction (st is then set to twice s). A SIMU restraint with dmax set to say 0.7 may be used to stabilize refinements in which there are overlapping disorder components with different PART numbers. This is complementary to RIGU which uses the connectivity table, and hence the PART rules to decide which atom pairs may be restrained. dx, dy and dz are the three principal dimensions of the crystal in mm, as usually quoted in publications. This information is written to the . cif file. If a SIZE instruction is present in the. ins file, SHELXL uses it to write the estimated minimum and maximum transmission to the. cif file. These estimates take into account that most of the diffraction from strongly absorbing crystals takes place at the edges and corners. All following atoms (until the next SPEC instruction) are considered to lie on special positions(for the purpose of automatic constraint generation) if they lie within del (Aring) of a special position. The coordinates of such an atom are also adjusted so that it lies exactly on the special position. STIR sres step0.01 The STIR instruction allows a stepwise improvement in the resolution. In the first refinement cycle, the high-resolution limit (i. e. lowest d) is set at sres, in the next cycle to (sresndashstep), in the next (sresndash2bullstep) etc. This continues until the limit of the data or the SHEL limit is reached, after which any remaining cycles to complete the number specified by CGLS or L. S. are completed with a constant resolution range. By starting at lower resolution and then gradually improving it, the radius of convergence for models with significant coordinate errors should be increased. This may be regarded as a primitive form of simulated annealing it could be useful in the early stages of refinement of molecular replacement solutions. SUMP c sigma c1 m1 c2 m2. The linear restraint: c c1fv(m1) c2fv(m2) . is applied to the specified free variables. This enables more than two atoms to be assigned to a particular site, with the sum of site occupation factors restrained to be a constant. It also enables linear relations to be imposed between distances used on DFIX restraints, for example to restrain a group of atoms to be collinear. sigma is the effective standard deviation. By way of example, assume that a special position on a four-fold axis is occupied by a mixture of sodium, calcium, aluminium and potassium cations so that the average charge is 2 and the site is fully occupied. The necessary restraints and constraints could be set up as follows (the program will take care of the special position constraints on the coordinates and U ij of course): This particular refinement would probably still be rather unstable, but the situation could be improved considerably by adding weak SUMP restraints for the elemental analysis. Such SUMP restraints may be used when elements are distributed over several sites in minerals so that the elemental composition corresponds (within suitable standard deviations) to an experimental chemical analysis. SUMP may also be applied to EXTI and BASF parameters, including parameters used to describe twinning (TWIN ). The parameters are counted in the order overall scale and free variables, EXTI. then BASF. The SWAT option allows two variables g and U to be refined in order to model diffuse solvent using Babinets principle (Moews amp Kretsinger, 1975). The calculated intensity is modified as follows: F c sup2(new) F c sup2(1 - g. exp-8pisup2U(sintheta lambda)sup2) A large value of U ensures that only the low theta F c sup2 values are affected. Subtracting the term in g in this way from the occupied regions of the structure is equivalent to adding a corresponding diffuse scattering term in the (empty) solvent regions in its effect on all calculated F c sup2 values except F(000). For proteins g usually refines to a value between 0.7 and unity, and U usually refines to a value between 2 and 5 for small molecules without significant diffuse solvent regions g should refine to zero. Since g and U are correlated, it is better to start the diffuse solvent refinement by giving SWAT with no parameters the program will then invent suitable starting values. Since both extinction and diffraction from diffuse solvent tend to affect primarily the strong reflections at low diffraction angle, they tend to show the same symptoms in the analysis of variance, and so a combined warning message is printed. It will however be obvious from the type of structural problem which of the two should be applied. The program does not permit the simultaneous refinement of SWAT and EXTI. SYMM symmetry operation Symmetry operators, i. e. coordinates of the general positions as given in International Tables. The operator x, y, z is always assumed, so may not be input. If the structure is centrosymmetric, the origin must lie on a center of symmetry. Lattice centering and the presence of an inversion center should be indicated by LATT. not SYMM. The symmetry operators may be specified using decimal or fractional numbers, e. g. 0.5-x, 0.5y, - z or Y-X, - X, Z16 the three components are separated by commas. Sets the temperature T of the data collection in degrees Celsius. This is reported to the . cif file and used to set the default isotropic U values for all atoms. TEMP must come before all atoms in the . ins file. TEMP also sets the default X-H bond lengths (see AFIX ) which depend slightly on the temperature because of librational effects. The default C-H bond lengths and default U-values are rounded to two decimal places so that they may be quoted more easily. Title of up to 76 characters, to appear at suitable places in the output. The characters and , if present, are part of the title and are not specially interpreted. TWIN 3x3 matrix -1 0 0 0 -1 0 0 0 -1 N2 N is the number of twin components (2 or greater) and the matrix is applied (iteratively if N gt 2) to generate the indices of the twin components from the input reflection indices, which apply to the first (prime) component. If a transformation matrix is also given on the HKLF instruction, it is applied first before the (iterative) application of the TWIN matrix. This method of defining twinning allows the standard HKLF 4 format to be used for the . hkl file, but can only be used when the reciprocal lattices of the original and twin-related components are superimposable. In other cases HKLF 5 format must be used. The F o sup2 values are fitted to the sum of k m F cm sup2 multiplied by the overall scale factor, where k 1 is one minus the sum of k 2. k 3. and the starting values for the remaining twin fractions k 2. k 3. are specified on a BASF instruction. Only one TWIN instruction is allowed. If BASF is omitted the TWIN factors are all assumed to be equal (i. e. perfect twinning). If the racemic twinning is present at the same time as normal twinning, N should be doubled (because there are twice as many components as before) and given a negative sign (to indicate to the program that the inversion operator is to be applied multiplicatively with the specified TWIN matrix). The number of BASF parameters, if any, should be increased from m-1 to 2m-1 where m is the original number of components (equal to N divided by 2). The TWIN matrix is applied m-1 times to generate components 2. m from the prime reflection (component 1) components m1. 2m are then generated as the Friedel opposites of components 1. m. Twin component number to be used for the completeness and Friedel completeness statistics. Only single or composite reflections containing this twin component are used for these statistics. It applies to both TWIN HKLF 4 and HKLF 5 data, but is most useful for the latter. The default N0 causes all components to be used. If there is no twinning, this parameter has no effect. Number of atoms of each type in the unit-cell, in SFAC order. WGHT a0.1 b0 c0 d0 e0 f.33333 The weighting scheme is defined as follows: w q sigmasup2(F o sup2) (aP)sup2 bP d esin(theta)lambda where P f Maximum of (0 or F o sup2) (1-f) F c sup2 . It is possible for the experimental F o sup2 value to be negative because the background is higher than the peak such negative values are replaced by 0 to avoid possibly dividing by a very small or even negative number in the expression for w. For twinned and powder data, the F c sup2 value used in the expression for P is the total calculated intensity obtained as a sum over all components. q is 1 when c is zero, expc(sin(theta)lambda)sup2 when c is positive, and 1 - expc(sin(theta)lambda)sup2 when c is negative. The use of P rather than (say) F o sup2 reduces statistical bias Wilson, Acta Cryst. A32 (1976) 994-996. The parameters should be set by trial and error so that the variance shows no marked systematic trends with the magnitude of F c sup2 or of resolution the program suggests a suitable WGHT instruction after the analysis of variance. This scheme is chosen to give a flat analysis of variance in terms of Fcsup2, but does not take the resolution dependence into account. It is usually advisable to retain default weights (WGHT 0.1) until all atoms have been found and the refinement is essentially complete, when the scheme suggested by the program can be used for the next refinement job by replacing the existing WGHT instruction by the one output by the program towards the end of the . res file. This procedure is adequate for most routine refinements. It may be desirable to use a scheme which does not give a flat analysis of variance to emphasize particular features in the refinement for example c 10 or -10 would weight up data at higher 2theta, e. g. to perform a high-angle refinement (uncontaminated by hydrogen atoms which contribute little at higher diffraction angle) prior to a difference electron density synthesis (FMAP 2) to locate the hydrogens. The exponential weights which are obtained when c is positive were advocated by Dunitz amp Seiler, Acta Cryst. B29 (1973) 589-595. Refinement against Fsup2 requires different weights to refinement against F in particular, making all the weights equal (unit weights), although useful in the initial stages of refinement against F, is never a sensible option for Fsup2. If the program suspects that an unsuitable WGHT instruction has been used it will output a warning message. WIGL del0.2 dU0.2 If WIGL is used, all atoms not on special positions are displaced by an average distance del Aring in a random direction. These shifts are applied after generating the connectivity table (which would otherwise be compromised) and before generating hydrogen atoms. Fixed coordinates (e. g. for special positions) are not changed. U iso and U 11. U 22 and U 33. but not U 23. U 13 and U 12 are multiplied by a random factor so that they change by an average of 100dU. WIGL is useful for removing R free memory effects and checking convergence properties. Shifts greater than about 0.5 Aring can result in some atoms moving out of density and not finding their way back home. If either parameter is given as negative. both random shifts are randomized (i. e. will be different each time the program runs). Writes the refined coordinates to a . pdb file. If n is positive hydrogen atoms are omitted if n is 1 all atoms are converted to isotropic and ATOM statements generated, and if n is 2 ANISOU statements are also generated (but B eq is still used on the ATOM statement). It is up to the user to ensure that the residue and atom names conform to PDB rules. Sets a lower bound for the eigenvalues of the U ij tensor of all anisotropic atoms or the U of an isotropic atom. The default (i. e. assumed if XNPD is not given) is XNPD -0.001. This has the effect that non-positive-definite (NPD) atoms are still detected and reported, but they are prevented from causing the refinement to explode. XNPD without a number sets Umin to 0.001, in which case no atom should be reported as NPD. The numbers of may be split and NPD atoms are output to the console at the end of the refinement. ZERR Z esd(a) esd(b) esd(c) esd(alpha) esd(beta) esd(gamma) Z value (number of formula units per cell) followed by the estimated standard deviations in the unit-cell dimensions. Z is only required for the CIF output the cell esds contribute to the estimated esds in bond lengths etc. after full-matrix refinement.