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即日起参与shelx97说明书翻译的虫子将给予金币奖励，翻译一段就给金币，多翻多得，任务上传中，敬请等待……想参与的可以先跟帖报个名 所有参与翻译的虫子都可以免金币获得最终版本，希望大家踊跃参与！ （by Moderator） 更多的译文详见 晶体论坛 http://15151.5d6d.com/ 第二章 Shelxl-结构精修 SHELXL是为晶体结构精修而编写的程序。虽然也可以解析尺寸在2.5 Å及更大的大分子化合物数据的结构，但主要是为了处理小分子结构而编写的。由于采用综合结构因子评价方法，因而在解析大分子结构时比传统的基于FFT法的大分子解析方法要慢得多。SHELXL非常易于安装和使用。这是一个使用广泛的程序，适于所有的空间群和各种类型的结构。极性轴限制与特殊位置限制可以自动的产生。该程序可以处理孪晶、复杂无序、绝对构型判定、CIF和PDB文件输出，还可以为困难精修控制提供大量不同的限制方法。SHELXPRO界面程序可以输出大分子的PS格式图片产生map和其他广泛大分子程序采用的格式。辅助程序CIFTAB利用cif文件产生小分子结构精修结果列表 2.1 Program organization 运行SHELXL程序，需要两个文件是必须的（ins文件，设置文件；hkl文件，衍射数据）；由于输入/输入文件均为ASCII文件，适合在不同的系统/联网上使用。在标准的SHELX格式的hkl文件中，包括h, k, l, F2 和 (F2)。程序可合并等效点并消除系统消光；但衍射数据的顺序并不重要。晶体数据，精修设置命令和原子的坐标等均被写入ins文件，另有一些文件格式比如说一些标准设置，特称为“include files”，但是这不是基础的。这些设置一般都放在原子名称、序号等前面，用四个字母的符号进行设置，这在以后的章节会有描述。对于所有的数据参数均有合理的默认值。SHELXL在任何操作系统上都可以利用写命令的方式正常运行。 shelxl name 对于任一个特定的结构，name是文件中的第一个组分。在有些操作系统上，name的长度不能超过8个字节。批操作一般需要用批命令行包括前面的命令。通过“PATH”建立路径来执行程序。没有环境变量的设置要求。 在精修处理界面上一些简要的处理过程被罗列出来，详细地信息被记录在lst文件中，该文件可打印或者用文档编辑软件打开。每一轮精修完成后，res文件被重新记录，ins文件只有的精修参数发生改变。可以拷贝或编辑用于下一轮的精修。在ins文件中加入MORE命令可控制精修时发送给lst文件中信息的数量，MORE的默认设置（不必写入）MORE 1 一般是合适的，但是MORE 3可为分析提供更多的诊断信息。ACT命令可产生可产生用于存档和出版的CIF格式文件。LIST 4 命令（由ACTA命令自动衍生）产生一个CIF格式的 2-1 衍射数据文件（x.fcf）。对于大分子结果输出文件PDB的产生，则用WPDB和LIST 6命令即可，当然是在SHELXPRO 子程序中完成的。 两种方式可以干扰正在运行的SHELXL程序。第一种方式是在MSDOD下运行时， “Ctrl+l”可以使其停止下来，但是不会丢失输出的临时文件，“Ctrl+c”则相反。按下Tab键也会产生类似于“Ctrl+l”的效果。在运行过程中用Esc键，程序会完成当前的最小二乘精修，接着计算此轮精修的结构因子、列表和傅立叶峰等等；否则Esc不会起作用。在计算机操作界面上没有“Esc”键， 第二种方式需要使用者建立X.fin文件（其内容倒不重要），程序会在一定间隔内删除它，而如果他起作用就会产生 2-2 2.2 设置文件 ins 所有的设置指令均采用含四个字节的命令，而其他信息则采用任意的格式，用一个或多个空格间隔开。大小写可以混用，但是开头的TITL命令行除外。TITL, CELL, ZERR, LATT (如需要), SYMM (如需要), SFAC, DISP (如需要) and UNIT指令的顺序必须固定，其他指令则放在UNIT与末指令HKLF之间。 有些指令需要关联到原子名，一般不加特定原子名称即代表所有的非氢原子。一系列的原子还可以用 fisrt atom > last atom 的方式，这表示处于期间的非氢原子均在其中被引用。 2.3衍射数据文件 X.hkl Hkl 文件中每一行具有相同的数据格式，均含有h,k,l,Fo2,(Fo2) 和一批数据。该文件以相同格式的一排数字0结尾。各个衍射数据之间不必相互区分，批数据会根据全景因子来对数据分组（可参见BASF指令）。衍射数据的顺序和批数据的数据顺序也是不重要的。与SHELX-76不同，SHELX-97 在每次运行时均重新读取hkl文件。程序在运行到ins文件中的HKLF指令时开始读取hkl衍射数据。HKLF指令专用于hkl格式文件，使得应用全景因子和reorientation 矩阵成为可能。运行时，程序假定hkl文件已经进行过洛仑兹、极化好吸收校正。需要指出的是对于劳埃和粉末数据的有专门的hkl扩展格式，另外对于孪晶数据仅靠加入TWIN指令也无法解决。 一般来说，hkl文件应包含测定数据而不进行消光排出或等效点合并。系统消光和Rint值可为空间群的判断正误提供一个良好的检查依据。因为在SHELXL在运行过程中时需要用刀复合的散射因子，因而在生成hkl文件时，Friedel opposites 通常不会被平均处理，但是当遇到处理大分子结构特别的异常散射时，是个例外。 2.4基于F2的精修 SHLXL通常采用基于F2的精修，即便输入的是F-值。对于大多数实验室生长的不完美晶体，基于F2的精修被证实优于基于F值的精修。需要考虑更队的实验信息而力图实现局部极小的可能就变小了。对赝对称的情况，往往是较弱的衍射就可以区分各种潜在的可能情况。由于当F2为0 或由于实验误差小于零时很难从(F2)估计(F)，因而无法进行基于全F-value的精修。 2-3 衍射实验测量强度和标准偏差，然后经过各种校正给出Fo2 和(Fo2)，如果您的数据还原程序只输出Fo 和(Fo)，那么您应当修正您的程序。. 利用HKLF 3 指令向SHELXL输入 Fo 和 (Fo) 也是合法操作。需要注意的是如果一个Fo2对满足方程F8.2 来说太大，那么就应使用方程F8.0。 使用阈值忽略弱衍射点的方法主要影响原子位移参数。通常在初期使用可以加速前几轮的精修，但是在最后精修时应采用所有衍射点。当然，属于系统错误的衍射点应删去（比如在最后精修中，OMIT命令可用于删除特定的衍射点，尽管并非没有好的解释， 但是所有的衍射点并不低于特定的阈值）。如果想不采用这些建议，可以参考Hirshfeld & Rabinovich (1973) 和 Arnberg, Hovmöller & Westman (1979) 中的报道。基于F2的精修还可以使孪晶结构、粉末数据及据对构型的确定更容易得到解决。 2.5 Initial processing of reflection data SHELXL可以自动的排出系统消光衍射，衍射数据的排序和合并由MERG指令控制。通常MERG 2（默认值） 指令适合小分子；等效衍射经合并，它们的指标被转换成为标准系统等效点，但是Friedel opposites在非心对称空间群中不被合并。MERG 4指令，合并Friedel opposites，设置所有元素的f"均为0，并为没有良好分散效应的生物大分子计数。 尽管处于统计学考虑，平方值可能会由于背景噪音大而为负值，但在我们整个文档中，人能够用Fo2代表实验测量。 Rint 和 Rsigma 的定义为: Rint = | Fo2 - Fo2(mean) | / [ Fo2 ] 其中两个总和包含所有输入衍射点及等效衍射点的平均值 Rsigma = [ (Fo2) ] / [ Fo2 ] 由于R-indices基于F2，他们一般会是基于F的指标的两倍。平均值的误差（表中不符合值）为rms偏差，来自平均值/（n-1）1/2，n值对应于给定的衍射点。考虑到合并衍射的(F2)，程序采用由综合独立组分的(F2)而得到的值，除非误差太大。 对一些孪晶结构的精修和批全景因子的最小二乘法精修来说，则应使用MERG 0 指令来避免等效衍射点的合并。 2-4 2.6 最小二乘精修 对于小分子来说往往采用全矩阵方法精修（在SHELXL中使用L.S.指令），这样在每轮精修后可得到最好的收敛，也允许适当的偏差。采用全矩阵精修所需要的CPU时间与衍射点数目和参数数目之积约成正比。这对大分子并不适用（较小的除外）。另外，当参数变得非常大时，单精度倒反矩阵还受到accumulated rounding误差的影响。一种较好的选择是采用共轭矩阵解决方案。这种方案只侧重包含限制的off-diagonal terms.这种方法被Konnert 和 Hendrickson (1980)应用于PROLSQ程序（但是对加速收敛进行了修正），与SHELXL (指令 CGLS)采用相同的运算法则。CGLS精修同样适用于中型或大型“小分子”的初期精修，需要很多轮才可以达到收敛，但是相当快速而有效。主要的缺点是不能提供有效标准偏差。 对L.S.和CGLS精修，均可实现block方法，即在每轮精修时使用不同混合的参数。例如，对于一个没有使用BLOC指令的CGLS精修，在最后一轮精修中可使用L.S. 1，DAMP 0 0 和 BLOC 1 （或者对蛋白质结构使用 BLOC N_1 > LAST），来获得所有几何参数的有效标准偏差；减少三个参数中的一个并使用一个较大的轮数，各相异性参数可以被固定。 2.7 R-指标和权重 基于F2 的精修的一个劣势是R-指标比基于F 的修正和OMIT阈值的要大(约两倍) 基于大于4(Fo)的F精修和传统指标也被输出出来。 wR2 = { [ w(Fo2–Fc2)2 ] / [ w(Fo2)2 ] }1/2 R1 = | |Fo| – |Fc| | / |Fo| Goodness of Fit 值也基于的F2精修: GooF = S = { [ w(Fo2–Fc2)2 ] / (n–p) }1/2 n 代表衍射点数，p代表精修中使用的参数的个数。 2-5 WGHT指令允许相当的弹性，但实践证明在精修基本完成前，可以保持权重值为默认值（0.1），然后采用程序建议值。这些参数给变量提供一个单调分析并使GOOF值趋近于1。 如果权重变化太快，则不易于收敛是因为出现象原子失去等造成的“权重下降”。对大分子来说，一般建议保留权重的默认值，对不完善的模型GOOF值大于1 也是可以接受的。 当写入不止两个WGHT参数时，权重方案简化为 w = 1 / [ 2(Fo2) + (aP)2 + bP ] 其中 P = [ 2Fc2 + Max(Fo2,0) ] / 3. 混合使用Fo2 and Fc2 被Wilson (1976)用来 减小统计偏差。 2.8 傅立叶合成 傅立叶合成的结果以峰列表的形式概括出来，可以编辑并用于下一轮精修的输入文件；或者以夯实打印形式来表示非键合作用等等。在每轮精修的结尾，采用差值电子密度法合成速度快而且诊断值比较可信。相比于SHELX-76，SHELXL可以自动寻找傅立叶合成的不对称单元，不论传统的或其他的设置，运算法则对所有空间群都是有效的。在傅立叶合成之前，Friedel opposites通常总是被合并而且采用散射校正，R1的计算基于合并的数据（没有阈的限制）。比(Fo)小的Fc衍射在傅立叶合成中是down-weighted。计算出的Rms 密度给出对噪音水平的估计。 2.9 关联矩阵（connectivity array） 程序自动产生氢原子、分子几何列表及限制等的关键因素是关联矩阵的存在。对于一个非无序结构的有机分子来说，关联矩阵可由标准原子半径来衍生出来。通过最小可能的干涉，简单的指令可以使得大多数无序情况的无序得以解决。每个原子被分配一个“PART”及数字n。 大多数情况下n=0，但是当存在无序组分时，也可采用其他值。对靠近的原子依据两种情况衍生出键来：（a）止一个n值为零；（b）两个n值为同一个制。关联矩阵可为精修自动添加对称操作。等效点的衍生可以由赋予阻止'PART'负值的方法。如果需要可以通过BIND或FREE来增删化学键。如果要衍生出与对称等效原子连接的额外的键，就需要用到EQIV指令。 2-6 2.10 列表 对小分子来说，使用BOND命令可以产生键长和键角列表，使用CONF命令产生尽可能多的扭转角。氢原子不属于自动产生的部分，但是用BOND $H可以在键长和键角中产生。 而用HTAB指令可以提供一种分析氢键的方法。程序允许选择指定的原子使用BOND和CONF指令，也可以使用RTAB指令（微生物大分子设计）。最小二乘平面和距离可由MPLA命令来实现。 用EQIV指令可以产生对称等效原子。 SHELXL输出的有效标准偏差考虑到晶胞的有效标准偏差，并由全斜方差矩阵来计算。唯一的例外是两个最小二乘平面间的夹角采用的是近似计算。需要注意的是阻尼精修会导致低估偏差。在特殊情况下，采用DAMP 0 0指令（没有阻尼，但是没有应用振幅）可以得到较低的有效标准偏差。 在SHELXL-97中，引入了HTAB指令来分析结构中的氢键问题。所有氢原子均参与氢键的寻找。HTAB指令的第二个形式是提供寻找对称操作的简便的方法，另外还可以解释可能放错位置的氢原子，例如不能确定氢原子或由于对两个不同O-H或N-H原子团上的氢原子自动设置成同一个氢键。HTAB指令的第二个形式中允许在其后加上D，A原子，对于供体原子还可以提供对称性代码。然后程序会寻找最合适的氢原子来形成氢键D-H•••A，然后向lst、cif文件中输出几何数据。 [ Last edited by lingzi326 on 2007-9-6 at 18:07 ] |
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（在线翻译，未完待续）4.7 Special facilities for -CH3 and -OH groups -CH3 and -OH 官能团专门的加氢指令 Methyl and hydroxyl groups are difficult to position accurately (unless neutron data are available!). 甲基和羟基官能团上的氢原子很难准确定位（除非有中子衍射的证据）。 If good (low-temperature) x-ray data are available, the method of choice is HFIX 137 for -CH3 and HFIX 147 for -OH groups; in this approach, a difference electron density synthesis is calculated around the circle which represents the locus of possible hydrogen positions (for a fixed X-H distance and Y-X-H angle). 当提供高质量的衍射数据时（如低温），可选择的方法是HFIX 137对-CH3 加氢，HFIX 147 对 -OH上的氧加氢，在这种方法中，每轮精修都会对代表氢原子可能位置的差值傅立叶峰进行计算。 The maximum electron density (in the case of a methyl group after local threefold averaging) is then taken as the starting position for the hydrogen atom(s). In subsequent refinement cycles (and in further least-squares jobs) the hydrogens are re-idealized at the start of each cycle, but the current torsion angle is retained; the torsion angles are allowed to refine whilst keeping the X-H distance and Y-X-H angle fixed (n=7). If unusually high quality data are available, AFIX 138 would allow the refinement of a common C-H distance for a methyl group but not allow the group to tilt; a variable metric rigid group refinement (AFIX 9 for the carbon followed by AFIX 135 before the first hydrogen) would allow it to tilt as well, but still retain tetrahedral H-C-H angles and equal C-H distances within the group. 最大的电子残余峰密度被认为是氢原子的最初位置，该位置上的氢原子在后面的精修步骤中会被继续理想化修正，但是夹角会保持原来的模式，扭转角在X-H和 Y-X-H 保持不变的情况下也参与精修（限制参数为n=7）。如果数据异常的好，指令 AFIX 138 会对甲基官能团的C-H间距进行限制，但不会带来甲基官能团的倾斜，刚性官能团精修（AFIX 9对碳进行限定，随后在第一个氢原子前加一个指令AFIX 135 ）可以使得甲基官能团倾斜，但同时保持四面体构型的 H-C-H夹角，并且在该官能团内C-H键长相等。 If the data quality is less good, then the refinement of torsion angles may not converge very well. In such cases the hydrogens can be positioned geometrically and refined using a riding model by HFIX 33 for methyl and HFIX 83 for hydroxyl groups. This staggers the methyl groups, and -OH groups attached to saturated carbons, as well as possible; -OH groups attached to aromatic rings are tested in one of the two positions with one hydrogen in the plane. In both cases the choice of hydrogen position is then determined by best hydrogen bond (to an N, O, Cl or F atom) that can be created. For disordered methyl groups (with two sites rotated by 60 degrees from one another) HFIX 123 is recommended, possibly with refinement of the corresponding site occupation factors via a 'free variable' so that their sum is unity (e.g. 21 and -21). 如果数据质量并不太好，那么扭转角的精修便不会收敛得太好。在这种情况下，可以用理论几何位置加氢，对于甲基采用指令HFIX 33 ，对于羟基采用指令HFIX 83。这样可能会使得甲基或连在饱和碳原子上的羟基产生摇摆，对于芳香环上的羟基加氢则要对两个可能的位置进行选择（因为处在苯环平面内，有两个位置可以用来确定氢原子：译者著），选择的标准是是否构成最佳氢键作用。对于无序的甲基基团（两个碳原子互为六十度角旋转）的情况，建议采用HFIX 123 指令，精修上可能要使用自由变量的位置占有率因子（SOF），模式例如21 和 -21等等。 The choice of a suitable (default) O-H distance is very difficult. O-H internuclear distances for isolated molecules in the gas phase are about 0.96 Å (cf. 1.10 for C-H), but the appropriate distance to use for X-ray diffraction must be appreciably shorter to allow for the displacement of the center of gravity of the electron distribution towards the oxygen atom, and also for librational effects. Although the (temperature dependent) value assumed by the program fits reasonably well for O-H groups in predominantly organic molecules, appreciably longer O-H distances are appropriate for low temperature studies of strongly (cooperatively) hydrogen-bonded systems; short H...O distances are always associated with long O-H distances. If there are many such O-H groups and good quality data are available, HFIX 88 (or 148) plus SADI restraints to make all the O-H distances approximately equal (with an esd of say 0.02) is a good approach. 选择合适的O-H距离比较困难。气相中孤立分子中O-H 核间距约为0.96A， [ Last edited by douvei on 2007-9-7 at 14:55 ] |
11楼2007-09-05 00:33:09
原文如下
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lingzi326(金币+20,VIP+0):恭喜你获得“晶体版热心虫友"二等奖！~~~
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2. SHELXL - Structure Refinement SHELXL is a program for the refinement of crystal structures from diffraction data, and is primarily intended for single crystal X-ray data of small moiety structures, though it can also be used for refinement of macromolecules against data to about 2.5 Å or better. It uses a conventional structure factor summation, so it is much slower (but a little more accurate) than standard FFT-based macromolecular programs. SHELXL is intended to be easy to install and use. It is very general, and is valid for all space groups and types of structure. Polar axis restraints and special position constraints are generated automatically. The program can handle twinning, complex disorder, absolute structure determination, CIF and PDB output, and provides a large variety of restraints and constraints for the control of difficult refinements. An interface program SHELXPRO enables macromolecular refinement results to be displayed in the form of Postscript plots, and generates map and other files for communication with widely used macromolecular programs. An auxiliary program CIFTAB is useful for tabulating the refinement results via the CIF output file for small molecules. 2.1 Program organization To run SHELXL only two input files are required (atoms/instructions and reflection data); since both these files and the output files are pure ASCII text files, it is easy to use the program on a heterogeneous network. The reflection data file (name.hkl) contains h, k, l, F2 and (F2) in standard SHELX format (section 2.3); the program merges equivalents and eliminates systematic absences; the order of the reflections in this file is unimportant. Crystal data, refinement instructions and atom coordinates are all input as the file name.ins; further files may be specified as 'include files' in the .ins file, e.g. for standard restraints, but this is not essential. Instructions appear in the .ins file as four-letter keywords followed by atom names, numbers, etc. in free format; examples are given in the following chapters. There are sensible default values for almost all numerical parameters. SHELXL is normally run on any computer system by means of the command: shelxl name where name defines the first component of the filename for all files which correspond to a particular crystal structure. On some systems, name may not be longer than 8 characters. Batch operation will normally require the use of a short batch file containing the above command etc. The executable program must be accessible via the 'PATH' (or equivalent mechanism). No environment variables or extra files are required. A brief summary of the progress of the structure refinement appears on the console, and a full listing is written to a file name.lst, which can be printed or examined with a text editor. After each refinement cycle a file name.res is (re)written; it is similar to name.ins, but has updated values for all refined parameters. It may be copied or edited to name.ins for the next refinement run. The MORE instruction controls the amount of information sent to the .lst file; normally the default MORE 1 is suitable, but MORE 3 should be used if extensive diagnostic information is required. The ACTA instruction produces CIF format files for archiving or electronic publication, and the LIST 4 instruction (generated automatically by ACTA) produces a CIF format reflection data file (name.fcf). For PDB deposition of macromolecular results, WPDB and LIST 6 should be used. The program SHELXPRO should then be used to complete the PDB file. Two mechanisms are provided for interaction with a SHELXL job which is already running. The first is used by the MSDOS and some other 'on-line' versions: if the The second mechanism requires the user to create the file name.fin (the contents of this file are irrelevant); the program tries at regular intervals to delete it, and if it succeeds it takes the same action as after |
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2.2 The .ins instruction file All instructions commence with a four (or fewer) character word (which may be an atom name); numbers and other information follow in free format, separated by one or more spaces. Upper and lower case input may be freely mixed; with the exception of the text string input using TITL, the input is converted to upper case for internal use in SHELXL. The TITL, CELL, ZERR, LATT (if required), SYMM (if required), SFAC, DISP (if required) and UNIT instructions must be given in that order; all remaining instructions, atoms, etc. should come between UNIT and the last instruction, which is always HKLF (to read in reflection data). A number of instructions allow atom names to be referenced; use of such instructions without any atom names means 'all non-hydrogen atoms' (in the current residue, if one has been defined). A list of atom names may also be abbreviated to the first atom, the symbol '>' (separated by spaces), and then the last atom; this means 'all atoms between and including the two named atoms but excluding hydrogens'. 2.3 The reflection data file name.hkl The .hkl file consists of one line per reflection in FORMAT(3I4,2F8.2,I4) for h,k,l,Fo2, (Fo2), and (optionally) a batch number. This file should be terminated by a record with all items zero; individual data sets within the file should NOT be separated from one another - the batch numbers serve to distinguish between groups of reflections for which separate scale factors are to be refined (see the BASF instruction). The reflection order and the batch number order are unimportant. This '.hkl' file is read each time the program is run; unlike SHELX-76, there is no facility for intermediate storage of binary data. This enhances computer independence and eliminates several possible sources of confusion. The .hkl file is read when the HKLF instruction (which terminates the .ins file) is encountered. The HKLF instruction specifies the format of the .hkl file, and allows scale factors and a reorientation matrix to be applied. Lorentz, polarization and absorption corrections are assumed to have been applied to the data in the .hkl file. Note that there are special extensions to the .hkl format for Laue and powder data, as well as for twinned crystals that cannot be handled by a TWIN instruction alone. In general the .hkl file should contain all measured reflections without rejection of systematic absences or merging of equivalents. The systematic absences and Rint for equivalents provide an excellent check on the space group assignment and consistency of the input data. Since complex scattering factors are used throughout by SHELXL, Friedel opposites should normally not be averaged in preparing this file; an exception can be made for macromolecules without significant anomalous scatterers. Note that SHELXS always merges Friedel opposites. 2.4 Refinement against F2 SHELXL always refines against F2, even when F-values are input. Refinement against ALL F2-values is demonstrably superior to refinement against F-values greater than some threshold [say 4(F)]. More experimental information is incorporated (suitably weighted) and the chance of getting stuck in a local minimum is reduced. In pseudo-symmetry cases it is very often the weak reflections that can discriminate between alternative potential solutions. It is difficult to refine against ALL F-values because of the difficulty of estimating (F) from (F2) when F2 is zero or (as a result of experimental error) negative. The diffraction experiment measures intensities and their standard deviations, which after the various corrections give Fo2 and (Fo2). If your data reduction program only outputs Fo and (Fo), you should correct your data reduction program, not simply write a routine to square the Fo values ! It is also legal to use HKLF 3 to input Fo and (Fo) to SHELXL. Note that if an Fo2 value is too large to fit format F8.2, then format F8.0 may be used instead. - the decimal point overrides the FORTRAN format specification. The use of a threshold for ignoring weak reflections may introduce bias which primarily affects the atomic displacement parameters; it is only justified to speed up the early stages of refinement. In the final refinement ALL DATA should be used except for reflections known to suffer from systematic error (i.e. in the final refinement the OMIT instruction may be used to omit specific reflections - although not without good reason - but not ALL reflections below a given threshold). Anyone planning to ignore this advice should read Hirshfeld & Rabinovich (1973) and Arnberg, Hovmöller & Westman (1979) first. Refinement against F2 also facilitates the treatment of twinned and powder data, and the determination of absolute structure. 2.5 Initial processing of reflection data SHELXL automatically rejects systematically absent reflections. The sorting and merging of the reflection data is controlled by the MERG instruction. Usually MERG 2 (the default) will be suitable for small molecules; equivalent reflections are merged and their indices converted to standard symmetry equivalents, but Friedel opposites are not merged in non-centrosymmetric space groups. MERG 4, which merges Friedel opposites and sets f" for all elements to zero, saves time for macromolecules with no significant dispersion effects. Throughout this documentation, Fo2 means the EXPERIMENTAL measurement, which despite the square may possibly be slightly negative if the background is higher than the peak as a result of statistical fluctuations etc. Rint and Rsigma are defined as follows: Rint = | Fo2 - Fo2(mean) | / [ Fo2 ] where both summations involve all input reflections for which more than one symmetry equivalent is averaged, and: Rsigma = [ (Fo2) ] / [ Fo2 ] over all reflections in the merged list. Since these R-indices are based on F2, they will tend to be about twice as large as the corresponding indices based on F. The 'esd of the mean' (in the table of inconsistent equivalents) is the rms deviation from the mean divided by the square root of (n-1), where n equivalents are combined for a given reflection. In estimating the (F2) of a merged reflection, the program uses the value obtained by combining the (F2) values of the individual contributors, unless the esd of the mean is larger, in which case it is used instead. For some refinements of twinned crystals, and for least-squares refinement of batch scale factors, it is necessary to suppress the merging of equivalent reflections with MERG 0. 2.6 Least-squares refinement Small molecules are almost always refined by full-matrix methods (using the L.S. instruction in SHELXL), which give the best convergence per cycle, and allows esd's to be estimated. The CPU time per cycle required for full-matrix refinement is approximately proportional to the number of reflections times the square of the number of parameters; this is prohibitive for all but the smallest macromolecules. In addition the (single precision) matrix inversion suffers from accumulated rounding errors when the number of parameters becomes very large. An excellent alternative for macromolecules is the conjugate-gradient solution of the normal equations, taking into account only those off-diagonal terms that involve restraints. This method was employed by Konnert & Hendrickson (1980) in the program PROLSQ; except for modifications to accelerate the convergence, exactly the same algorithm is used in SHELXL (instruction CGLS). The CGLS refinement can be also usefully employed in the early stages of refinement of medium and large 'small molecules'; it requires more cycles for convergence, but is fast and robust. The major disadvantage of CGLS is that it does not give esds. For both L.S. and CGLS options, it is possible to block the refinement so that a different combination of parameters is refined each cycle. For example after a large structure has been refined using CGLS (without BLOC), a final job may be run with L.S. 1, DAMP 0 0 and BLOC 1 (or e.g. BLOC N_1 > LAST for a protein) to obtain esds on all geometric parameters; the anisotropic displacement parameters are held fixed, reducing the number of parameters by a factor of three and the cycle time by an order of magnitude. 2.7 R-indices and weights One cosmetic disadvantage of refinement against F2 is that R-indices based on F2 are larger than (more than double) those based on F. For comparison with older refinements based on F and an OMIT threshold, a conventional index R1 based on observed F values larger than 4(Fo) is also printed. wR2 = { [ w(Fo2–Fc2)2 ] / [ w(Fo2)2 ] }1/2 R1 = | |Fo| – |Fc| | / |Fo| The Goodness of Fit is always based on F2: GooF = S = { [ w(Fo2–Fc2)2 ] / (n–p) }1/2 where n is the number of reflections and p is the total number of parameters refined. The WGHT instruction allows considerable flexibility, but in practice it is a good idea to leave the weights at the default setting (WGHT 0.1) until the refinement is essentially complete, and then to use the scheme recommended by the program. These parameters should give a flat analysis of variance and a GooF close to unity [there was a bug in SHELXL-93 that can occasionally cause the program to abort when trying to estimate the new weighting parameters, though it appeared to happen only with poor quality data or the wrong solution]. If the weights are varied too soon, the convergence may be impaired, because features such as missing atoms are 'weighted down'. For macromolecules it may be advisable to leave the weights at the default settings; and to accept a GooF greater than one as an admission of inadequacies in the model. When not more than two WGHT parameters are specified, the weighting scheme simplifies to: w = 1 / [ 2(Fo2) + (aP)2 + bP ] where P is [ 2Fc2 + Max(Fo2,0) ] / 3. The use of this combination of Fo2 and Fc2 was shown by Wilson (1976) to reduce statistical bias. It may be desirable to use a scheme that does not give a flat analysis of variance to emphasize particular features in the refinement, for example by weighting up the high angle data to remove bias caused by bonding electron density (Dunitz & Seiler, 1973). 2.8 Fourier syntheses Fourier syntheses are summarized in the form of peak-lists (which can be edited and re-input for the next refinement job), or as 'lineprinter plots' with an analysis of non-bonded interactions etc. It is recommended that a difference electron density synthesis is performed at the end of each refinement job; it is quick and of considerable diagnostic value. In contrast to SHELX-76, SHELXL finds the asymmetric unit for the Fourier synthesis automatically; the algorithm is valid for all space groups, in conventional settings or otherwise. Before calculating a Fourier synthesis, the Friedel opposites are always merged and a dispersion correction applied; a value of R1 is calculated for the merged data (without a threshold). Reflections with Fc small compared to (Fo) are down-weighted in the Fourier synthesis. The rms density is calculated to give an estimate of the 'noise level' of the map. 2.9 The connectivity array The key to the automatic generation of hydrogen atoms, molecular geometry tables, restraints etc. is the connectivity array. For a non-disordered organic molecule, the connectivity array can be derived automatically using standard atomic radii. A simple notation for disordered groups enables most cases of disorder to be processed with a minimum of user intervention. Each atom is assigned a 'PART' number n. The usual value of n is 0, but other values are used to label components of a disordered group. Bonds are then generated for atoms that are close enough only when either (a) at least one of them has n=0, or (b) both values of n are the same. A single shell of symmetry equivalents is automatically included in the connectivity array; the generation of equivalents (e.g. in a toluene molecule on an inversion center) may be prevented by assigning a negative 'PART' number. If necessary bonds may be added to or deleted from the connectivity array using the BIND or FREE instructions. To generate additional bonds to symmetry equivalent atoms, EQIV is also needed. 2.10 Tables For small structures, bond lengths and angles for the full connectivity array may be tabulated with BOND, and all possible torsion angles with CONF. Although hydrogen atoms are not normally included in the connectivity array, they may be included in the bond lengths and angles tables by BOND $H. Alternatively HTAB produces a convenient way of analysing hydrogen bonds. It is also possible to be selective by naming specific atoms on the BOND and CONF instructions, or by using the RTAB instruction (which was designed with macromolecules in mind). Least-squares planes and distances of (other) atoms from these planes may be generated with MPLA. Symmetry equivalent atoms may be specified on any of these instructions by reference to EQIV symmetry operators. All esds output by SHELXL take the unit-cell esds into account and are calculated using the full covariance matrix. The only exception is the esd in the angle between two least-squares planes, for which an approximate treatment is used. Note that damping the refinement (see above) leads to underestimates of the esds; in difficult cases a final cycle may be performed with DAMP 0 0 (no damping, but no shifts applied) to obtain good esds. The HTAB instruction has been introduced in SHELXL-97 to analyze the hydrogen bonding in the structure. A search is made over all hydrogen atoms to find possible hydrogen bonds. This is a convenient way of finding the symmetry operations necessary for the second form of HTAB instructions (needed to obtain esds and CIF output), and also reveals potential misplaced hydrogens, e.g. because they do not make any hydrogen bonds, or because the automatic placing of hydrogen atoms has assigned the hydrogens of two different O-H or N-H groups to the same hydrogen bond. In the second form of the HTAB instruction, HTAB is followed by the names of the donor atom D and the acceptor atom A; for the latter a symmetry operation may also be specified. The program then finds the most suitable hydrogen atom to form the hydrogen bond D-H•••A, and outputs the geometric data for this hydrogen bond to the .lst file and the .cif file (if ACTA is present). |
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4.6 Hydrogen atom generation and refinement It is difficult to locate hydrogen atoms accurately using X-ray data because of their low scattering power, and because the corresponding electron density is smeared out, asymmetrical, and is not centered at the position of the nucleus. In addition hydrogen atoms tend to have larger librational amplitudes than other atoms. For most purposes it is preferable to calculate the hydrogen positions according to well-established geometrical criteria and then to adopt a refinement procedure which ensures that a sensible geometry is retained. The above table summarizes the options for generating hydrogen atoms; the hydrogen coordinates are re-idealized before each cycle. The distances given in this table are the values for room temperature, they are increased by 0.01 or 0.02 Å for low temperatures (specified by the TEMP instruction) to allow for the smaller librational correction at low temperature. 4.6 氢原子产生和精修 使用X-射线数据很难准确地找出氢原子得位置，是由于氢原子非常弱的衍射能力电子密度非常小, 不对称且不集中。另外氢原子比其他原子倾向于产生更大的振幅。因而更多情况下按照几何知识计算氢位置显得更好，在后面的精修过程中只需要保持精准的几何构型就可以了。上述的列表总结了产生氢原子的设置; 在每轮精修前，氢原子的座标被重新理想化计算。表中给出的距离是平均值，室温下这些距离会变长，低温下通过temp指令可以引起精修过程中较小振幅的变化。 [ Last edited by douvei on 2007-9-5 at 00:32 ] |
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第7章这段我领走
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7. SHELXL Instruction Summary This chapter lists the instructions that may be used in the .ins file for SHELXL-97. Defaults are given in square brackets; '#' indicates that the program will generate a suitable default value based on the rest of the available information. Continuation lines are flagged by '=' at the end of a line, the instruction being continued on the next line which must start with one or more spaces. Other lines beginning with spaces are treated as comments, so blank lines may be added to improve readability. All characters following '!' or '=' in an instruction line are ignored. The .ins file may include an instruction of the form: +filename (the '+' character MUST be in column 1). This causes further input to be taken from the named file until an END instruction is encountered in that file, whereupon the file is closed and instructions are taken from the next line of the .ins file. The input instructions from such an 'include' file are not echoed to the .lst and .res file, and may NOT contain FVAR, BASF, EXTI or SWAT instructions or atoms (except inside a FRAG...FEND section) since this would prevent the .res file from being used unchanged for the next refinement job (after renaming as .ins). The '+filename' facility enables standard fragment coordinates or long lists of restraints etc. to be read from the same files for each refinement job, and for different structures to access the same fragment or restraint files. One could also for example store the LATT and SYMM instructions for different space groups, or neutron scattering factors for particular elements, or LAUE instructions followed by wavelength-dependent scattering factors, in suitably named files. Since these 'include' files are not echoed, it is a good idea to test them as part of an .ins file first, to check for possible syntax errors. Such 'include' files may be nested; the maximum allowed depth depends upon the operating system and compiler used. [ Last edited by lingzi326 on 2007-9-6 at 19:42 ] |
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lingzi32613楼
2007-09-06 11:33
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2007-09-22 01:33
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