Olex2中解析程序额外解析设置

DJ_Tokyo

ShelXD-DualSpace

NTRY ntry [0]
Number  of global tries if starting from random atoms, PATS or GROP. If ntry is zero  or absent, the program runs until it is interrupted by writing a name.fin file in the current working  directory.	如果从随机原子、PATS或GROP开始，则全局尝试次数。如果ntry为零或不存在，则程序将运行，直到在当前工作目录中写入name.fin文件而中断为止。

FIND na [0], ncy [#]
Search  for na atoms in ncy dual space  cycles. If WEED is employed, na is  the number of atoms remaining after the random omit. ncy defaults to the largest of (20 or na) or, if PATS is used, to  the smaller of (3na and 20). If  FIND is absent, PLOP expands directly from the starting atoms.	在ncy双空间循环中寻找na个原子。如果使用WEED，na是随机省略后剩余的原子数。ncy默认为（20或na）中的最大值，如果使用PATS，则默认为（3na和20）中的较小值。如果不存在FIND，PLOP将直接从起始原子展开。

Note: Olex2  calculates a sensible default value for na  based on the cell volume.

注：Olex2根据晶胞体积计算na的合理默认值。

MIND mdis [1.0], mdeq [2.2]

|mdis| is the shortest distance allowed  between atoms for PATS and FIND. If mdis  is negative PATFOM is calculated,  and the crossword table for the  best PATFOM value so far is output to the .lst  file. In this case the solution is passed on to the PLOP stage if either the  CC is the best so far or the PATFOM  is the best so far. mdeq is the  minimum distance between symmetry equivalents for FIND (for PATS the |mdis| distance is used). Thus the  default setting of mdeq prevents  FIND from placing atoms on special positions. This is usually desirable  because it helps to avoid pseudo-solutions such as the 'uraninum atom  solution' that are incorrect but fit the tangent formula, but it might be  better to change this setting to -0.1 to allow special positions; especially  for the location of heavy atom sites obtained by (halide) soaking. For PLOP  the PREJ instruction can be used to control whether peaks on special  positions are selected.

|mdis|是PATS和FIND原子之间允许的最短距离。如果mdis为负，则计算PATFOM，并将迄今为止最佳PATFOM值的填字游戏表输出到.lst文件。在这种情况下，如果CC是迄今为止最好的，或者PATFOM是迄今为止最佳的，则将解析解传递到PLOP阶段。mdeq是FIND的对称等价物之间的最小距离（对于PATS，使用|mdis|距离）。因此，mdeq的默认设置阻止FIND将原子放置在特殊位置。这通常是可取的，因为它有助于避免伪解，如“铀原子解”，这些伪解是不正确的，但符合正切公式，但最好将此设置更改为-0.1，以允许特殊位置；特别是用于通过（卤化物）浸泡获得的重原子位点的定位。对于PLOP，PREJ指令可用于控制是否选择了特殊位置上的峰值。

PLOP followed by up to 10 numbers	PLOP后最多有10个数字
PLOP  specifies the number of peaks to start with in each cycle of the peaklist optimization algorithm of  Sheldrick & Gould (1995). Peaks are then eliminated one at a time until  either the correlation coefficient cannot be increased any more or 50% of the  peaks have been eliminated.	PLOP指定了Sheldrick &  Gould（1995）的峰值优化算法的每个周期中要开始的峰值数量。然后一次消除一个峰值，直到相关系数不能再增加或者50%的峰值已经消除。

Note: Olex2  calculates sensible default values based on the cell volume.

注：Olex2根据晶胞体积计算合理的默认值。

ShelXS-DirectMethods

TREF np [100] nE [#] kapscal [#]  ntan [#] wn [#]

np is  the number of direct methods attempts; if negative, only the solution with  code number |np| is generated (the code number is in fact a random number  seed). Since the random number generation is very machine dependent, this can  only be relied upon to generate the same results when run on the same model  of computer. This facility is used to generate E-maps for solutions which do  not have the 'best' combined figure of merit. No other parameter may be  changed if it is desired to repeat a solution in this way. For difficult  structures, it may well be necessary to increase np (e.g. TREF 5000) and of  course the computer time allocated for the job.

np是直接法尝试的次数；如果为负数，则只生成代码为|np|的解（代码实际上是一个随机数种子）。由于随机数的生成非常依赖于机器，因此只有在同一型号的计算机上运行时才能生成相同的结果。此功能用于为不具有“最佳”综合诊断指标的解决方案生成E图。如果希望以这种方式重复解析，则不得更改其他参数。对于困难的结构，很可能有必要增加np（例如TREF 5000），当然还有分配给作业的计算机时间。

nE  reflections are employed in the full tangent formula phase refinement. Values  of nE that give fewer than 20 unique phase relations per reflection for the  full phase refinement are not recommended.

nE个衍射点被用于全正切公式的相位精修。对于全相位精修，不推荐每次衍射点给出少于20个唯一相位关系的nE值。

kapscal  multiplies the products of the three E-values used in triplet phase  relations; it may be regarded as a fudge factor to allow for experimental  errors and also to discourage overconsistent (uranium atom) solutions in  symorphic space groups. If it is negative the cross-term criteria for the  negative quartets are relaxed (but all three cross-term reflections must  still be measured), and more negative quartets are used in the phase  refinement, which is also useful for symorphic space groups.

kapscal乘以三重相位关系中使用的三个E值的乘积；它可以被视为一个经验系数，以允许实验误差，并阻止对称空间群中的超一致（铀原子）解。如果它是负的，则放宽负四分之一的交叉项标准（但仍必须测量所有三个交叉项衍射点），并且在相位精修中使用更多的负四分一，这对对称空间群也很有用。

ntan is  the number of cycles of full tangent formula refinement, which follows the  phase annealing stage and involves all nE reflections; it may be increased  (at the cost of CPU time) if there is evidence that the refinement is not  converging well. The tangent formula is modified to avoid overconsistency by  applying a correction to the resulting phase of cos-1(<α>/α)  when <α> is less than α ; the sign of the correction is chosen to give  the best agreement with the negative quartets (a random sign is used if there  are no negative quartets involving the phase in question). This tends to  drive the figures of merit Rα  and Nqual simultaneously to desirable values. If ntan is negative, a penalty  function of (<Σ1> - Σ1)2 is added to  CFOM (see below) if and only if Σ1 is less than its estimated  value <Σ1>. Σ1 is a weighted sum of the products  of the expected and observed signs of one-phase seminvariants, normalized so  that it must lie in the range -1 to +1. This is useful (i.e. better than  nothing) if no negative quartets have been found or if they are unreliable,  e.g. when macromolecular ΔF data  are employed (see below).

ntan是全正切公式精修的循环数，其遵循相位退火阶段并涉及所有nE个衍射点；如果有证据表明精修没有很好地收敛，则它可能会增加（以CPU时间为代价）。当<α>小于α时，通过对cos-1(<α>/α)的最终相位进行校正，修改切线公式以避免过度一致性；选择校正的符号以给出与负四分之一的最佳一致性（如果不存在涉及所述相位的负四分一，则使用随机符号）。这往往会使品质因子Rα和Nqual同时达到理想值。如果ntan为负，则(<Σ1>  - Σ1)2的罚函数被添加到CFOM（见下文），当且仅当Σ1小于其估计值<Σ1>。Σ1是一个相位半变量的预期符号和观测符号的乘积的加权和，归一化后它必须在-1到+1的范围内。如果没有发现负四分之一或它们不可靠，例如当使用大分子ΔF数据时，这是有用的（即总比没有好）（见下文）。

wn is a  parameter used in calculating the combined figure of merit CFOM: CFOM = Rα (NQUAL < wn) or Rα + (wn-NQUAL)2  (NQUAL ≥ wn); wn should be about 0.1 more negative than the anticipated value  of NQUAL. If it is known that the measurements of the weak reflections are  unreliable (i.e. have high standard deviations), e.g. because data were  collected using the default options on a CAD-4 diffractometer, then the NQUAL  figure of merit is less reliable. If the space group does not possess  translation symmetry, it is essential to obtain good negative quartets, i.e.  to measure ALL reflections for an adequate length of time.

wn是用于计算综合诊断指标CFOM的参数：CFOM = Rα (NQUAL < wn)或Rα +  (wn-NQUAL)2 (NQUAL ≥ wn)；wn应该比NQUAL的预期值更负0.1左右。如果已知弱衍射点的测量是不可靠的（即具有高标准偏差），例如因为数据是使用CAD-4衍射仪上的默认选项收集的，那么NQUAL品质因子就不那么可靠了。如果空间群不具有平移对称性，则必须获得良好的负四分之一，即在足够长的时间内测量所有衍射点。

Only  the TREF instruction is essential to specify direct methods; appropriate  INIT, PHAN, FMAP, GRID and PLAN instructions are then generated automatically  if not given. ShelX-97 Manual

只有TREF指令对于指定直接方法是必不可少的；如果没有给出，则自动生成适当的INIT、PHAN、FMAP、GRID和PLAN指令。ShelX-97手册

INIT nn [#] nf [#] s+ [0.8] s-  [0.2] wr [0.2]

The  first stage involves five cycles of weighted tangent formula refinement  (based on triplet phase relations only) starting from nn reflections with  random phases and weights of 1. Single phase seminvariants which have Σ1-formula  P+ values less that s- or greater than s+  are included with their predicted phases and unit weights. All these  reflections are held fixed during the INIT stage but refined freely in the  subsequent stages. The remaining reflections also start from random phases  with initial weights wr, but both the phases and the weights are allowed to  vary.

第一阶段包括从具有随机相位和权重为1的nn个衍射点开始的五个加权正切公式精修周期（仅基于三重相位关系）。Σ1-公式P+值小于s-或大于s+的单相半变量包含在其预测相位和单位权重中。所有这些衍射点在INIT阶段保持固定，但在随后的阶段自由精修。剩余的衍射点也从初始权重为wr的随机相位开始，但相位和权重都允许变化。

If  nf is non-zero, the nf 'best' (based on the negative quartet and triplet  consistency) phase sets are retained and the process repeated for (npp-nf)  parallel phase sets, where npp is the previous number of phase sets processed  in parallel (often 128). This is repeated for nf fewer phase sets each time  until only a quarter of the original number are processed in parallel. This  rather involved algorithm is required to make efficient use of available  computer memory. Typically nf should be 8 or 16 for 128 parallel  permutations.

如果nf为非零，则保留nf“最佳”（基于负四重态和三重态一致性）相位集，并对（npp-nf）并行相集重复该过程，其中npp是并行处理的先前相位集数量（通常为128）。每次对nf个较少的相位集重复此操作，直到只有原始数量的四分之一被并行处理。需要这种相当复杂的算法来有效地利用可用的计算机存储器。通常，对于128个并行排列，nf应该是8或16。

The  purpose of the INIT stage is to feed the phase annealing stage with  relatively self-consistent phase sets, which turns out to be more efficient  than starting the phase annealing from purely random phases. If TREF 0 is  used to generate partial structure phases for all reflections, the INIT stage  is skipped. To save time, only ns reflections and the strongest mtpr triplets  for each reflection (or less, if not so many can be found) are used in the  INIT stage; these numbers are given on the PHAN instruction. ShelX-97 Manual

INIT阶段的目的是为相退火阶段提供相对自洽的相位集，这比从纯随机相位开始相位退火更有效。如果TREF  0用于为所有衍射点生成部分结构相位，则跳过INIT阶段。为了节省时间，在INIT阶段中仅使用ns个衍射点和每个衍射点的最强mtpr三重态（或者更少，如果不能找到那么多的话）；这些数字在PHAN指令中给出。ShelX-97手册

PHAN steps [10] cool [0.9] Boltz  [#] ns [#] mtpr [40] mnqr [10]

The  second stage of phase refinement is based on 'phase annealing' (Sheldrick,  1990. This has proved to be an efficient search method for large structures,  and possesses a number of beneficial side-effects. It is based on steps  cycles of tangent formula refinement (one cycle is a pass through all ns  phases), in which a correction is applied to the tangent formula phase. The  phase annealing algorithm gives the magnitude of the correction (it is larger  when the 'temperature' is higher; this corresponds to a larger value of  Boltz), and the sign is chosen to give the best agreement with the negative  quartets (if there are no negative quartets involving the reflection in  question, a random sign is used instead). After each cycle through all ns  phases, a new value for Boltz is obtained by multiplying the old value by  cool; this corresponds to a reduction in the 'temperature'. To save time,  only ns reflections are refined using the strongest b> mtpr triplets and  b> mnqr quartets for each reflection (or less, if not so many phase  relations can be found). The phase annealing parameters chosen by the program  will rarely need to be altered; however if poor convergence is observed, the  b> Boltz value should be reduced; it should usually be in the range 0.2 to  0.5. When the 'TEXP 0 / TREF' method of multisolution partial structure  refinement is employed, Boltz should be set at a somewhat higher value (0.4  to 0.7) so that not too many solutions are duplicated. ShelX-97 Manual

相位精修的第二个阶段基于"相位退火"  (Sheldrick, 1990)。这已被证明是一种有效的大分子结构搜索方法，并具有许多有益的副作用。它基于切线公式精修的步骤循环(一个循环通过所有ns个相位)，其中对切线公式阶段应用校正。相位退火算法给出了校正量("温度"越高校正量越大；这对应于一个更大的Boltz值)，并选择该符号来给出与负四重态的最佳一致性(若所讨论的衍射点没有涉及负四重态，则使用随机符号)。在经历过所有ns个相位的每个循环之后，通过将旧值乘以cool得到Boltz的新值；这对应于"温度"的降低。为节省时间，对每个衍射点的最强mtpr三重态和mnqr四重态用于仅对ns个衍射点精修(或更少，若找不到那么多相位相关的话)。程序选择的相位退火参数很少需要改变；但若观察到收敛性差，则应当减小Boltz值；它通常应当在0.2到0.5之间。当采用多重解析部分结构精修的"TEXP  0 / TREF"方法时，应当将Boltz设为较高的值(0.4到0.7)以避免重复太多的解析。ShelX-97手册

ESEL Emin [1.2] Emax [5] dU [.005]  renorm [.7] axis [0]
Emin  sets the minimum E-value for the  list of largest E-values which the  program normally retains in memory; it should be set so as to give more than  enough reflections for TREF etc. It is also the threshold used for tangent  expansion and 'peak-list optimisation'. It is advisable to reduce Emin to  about 1.0 for triclinic structures and pseudosymmetry problems. If Emin is  negative, acentric triclinic data are generated for use in all calculations.  The other parameters control the normalisation of the E-values:	Emin为程序通常保留在内存中的最大E值列表设置最小E值；它的设置应当确保为TREF等提供足够多的衍射点。它也是切线扩展和"峰列表优化"使用的阈值。对于三斜结构和赝对称问题，建议将Emin降低至1.0左右。若Emin为负，则生成用于所有计算的非中心三斜数据。其他参数控制的E值的标准化：
new(E)  = old(E) • exp[ 8dU (πsinθ/λ)2  ] / [ old(E)-4 + Emax-4  ]0.25
renorm  is a factor to control the parity group renormalisation; 0.0 implies no  renormalisation, 1.0 sets full renormalisation, i.e. the mean value of E2  becomes unity for each parity group.	renorm是控制奇偶群再归一化的一个因子；0.0表示没有再归一化，1.0设置完全再归一化，即每个奇偶群的E2平均值变为1。
If  axis is 1, 2 or 3, an additional similar renormalisation is applied for  groups defined by the absolute value of the h, k or l index respectively. If  axis is set to zero, no such additional renormalisation is applied. ShelX-97 Manual	如果axis为1、2或3，则对分别由h、k或l指数的绝对值定义的群应用额外的类似再归一化。若axis设为零，则不应用此额外的再归一化。ShelX-97手册

EGEN d(min) d(max)

All  missing reflections in the resolution range d(min) to d(max) Å (the order of  d(min) and d(max) is unimportant) are generated on a statistical basis,  assuming that they were skipped during the data collection because a prescan  indicated that they were weak. These reflections will then be flagged as  'unobserved', but improve the estimation of the remaining E-values and enable an increased  number of negative quartets to be identified. d(min) should be safely inside  the resolution limit of the data and d(max) should be set so that there is no  danger of regenerating strong reflections (as weak) which were cut off by the  beam stop etc. ShelX-97 Manual

分辨率范围d(min)  Å到d(max)  Å（(d(min)和d(max)的顺序不重要）内的所有缺失衍射点是在统计基础上生成的，假设它们在数据收集过程中被跳过，因为预扫描表明它们很弱。然后，这些衍射点被标记为"未观测到的"，但提高了对其余E值的估计，并使得能够识别更多的负四重态。d(min)应当安全地在数据的分辨率限制内，d(max)的设置应当确保不存在再产生被光束挡板等截断的强衍射点(弱衍射点)的危险。ShelX-97手册

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. Note that the grid is 53 x 53 x nl points, i.e.  twice as large as in SHELX-76, and that sl and dl need not be integral. The  103 x 103 x nl grid is only available when it is set automatically by the  program (see above). ShelX-97 Manual

傅立叶网格，不自动设置时。起点和增量乘以100。s为起始值，d为增量，l为垂直于层的方向，a为从左至右穿过纸面，d为从上到下穿过纸面。请注意，网格是53 ×  53 × nl点，即是SHELX-76中的两倍大，并且sl和dl不需要积分。103 × 103 × nl网格只有在程序自动设置时才可用(见上文)。ShelX-97手册

ShelXS-PattersonMethod

PATT nv [#] dmin [#] resl [#] Nsup  [#] Zmin [#] maxat [#]
nv is  the number of superposition vectors to be tried; if it is negative the search  for possible origin shifts is made more exhaustive by relaxing various  tolerances etc.	nv为将要尝试的叠加向量数；若为负，则通过放宽各种公差等使对可能的原点偏移的搜索更加详尽。

dmin is  the minimum allowed length for a heavy-atom to heavy-atom vector; it affects  ONLY the choice of superposition vector. If it is negative, the program does  not generate any atoms on special positions in stage 4 (useful for some  macromolecular problems).

dmin为重原子到重原子矢量的最小允许长度；它仅影响叠加向量的选择。若其为负，程序不会在第4阶段中在特殊位置生成任何原子（对于某些大分子问题有用）。

resl is  the effective resolution in Å as deduced from the reflection data, and is  used for setting various tolerances. If the data extend further than the  crystal actually diffracted, or if the outer data are incomplete, it may well  be worth increasing this number. This parameter can be relatively critical  for macromolecular structures.

resl为从衍射数据推断的以Å为单位的有效分辨率，并用于设置各种公差。若数据比晶体实际的衍射延伸得更远，或者若外部数据不完整，则增加这个数字可能是值得的。此参数对大分子结构来说相对重要。

Nsup is  the number of unique peaks to be found by searching the superposition  function.

Nsup为通过搜索叠加函数找到的独立峰数目。

Zmin is  the minimum atomic number to be included as an atom in the crossword table  etc. (if this is set too low, the calculation can take appreciably longer).

Zmin为将要包含在纵横字谜表等中的最小原子数（如果此值设置过低，计算可能会花费相当长时间）。

maxat is  the maximum number of potential atoms to be included in the crossword table,  and can also appreciably affect the time required for PATT.

maxat为将要包含在纵横字谜表中的潜在原子的最大数目，并且还可以明显影响PATT所需的时间。

VECT X Y Z

A  superposition vector (with coordinates taken from the Patterson peak-list)  may be input by hand by a VECT instruction, in which case the first two  numbers on the PATT instruction will be automatically generated if not  present in the .ins file. There may be any number of VECT instructions.  parameter negative and/or by increasing the value of resl a little. The sign  of the second PATT parameter (a negative sign excludes atoms on special  positions) and the list of elements which might be present (SFAC/UNIT) should  perhaps also be reconsidered. ShelX-97 Manual

叠加矢量（坐标取自Patterson峰值列表）可以通过VECT指令手动输入，在这种情况下，如果在.ins文件中不存在，PATT指令上的前两个数字将自动生成。VECT指令可以有任意数量。参数为负和/或通过稍微增加resl的值。第二个PATT参数的符号（负号不包括特殊位置上的原子）和可能存在的元素列表（SFAC/UNIT）可能也应该重新考虑。ShelX-97手册

ESEL、EGEN和GRID同ShelXS-DirectMethods，见上文。

ShelXS-StructureExpansion

TEXP na [#] nH [0] Ek [1.5]

na  PHAS reflections with Eo  > Ek and the largest values of Ec/Eo are generated for use in  partial structure expansion or direct methods. The first nH atoms (heavy  atoms) in the atom list are retained during partial structure expansion, the  rest are thrown away after calculating phases. At least one atom MUST be  given! TEXP automatically generates appropriate FMAP, GRID and PLAN  instructions.

生成na个Eo >  Ek以及具有最大Ec/Eo值的PHAS衍射点用于部分结构扩展或直接法。原子列表中的第一个nH原子(重原子)在部分结构扩展中被保留，其余的在计算相位后被丢弃。必须给定至少一个原子！TEXP自动生成适当的FMAP、GRID和PLAN指令。

TEXP  (and/or PHAS) may be used in conjunction with TREF to generate fixed phases for  use in direct methods; the special TEXP option na = 0 provides point atom  phases for ALL reflections, which are then refined during the phase annealing  and tangent expansion stages of direct methods (as specified on the PHAN and  TREF instructions). It is not necessary to use different starting phases for  the different phase sets, because the phase annealing stage itself introduces  (statistically distributed) random phase shifts! This is a powerful method of  partial structure expansion for cases when the phasing power of the partial  structure is not quite adequate, e.g. when it consists of only one atom (say  P or S in a large organic structure). If at least 5 atoms have been correctly  located then TEXP alone should suffice.

TEXP(和/或PHAS)可与TREF结合使用以生成用于直接法的固定相位；特殊的TEXP选项na = 0为所有衍射点提供点原子相位，然后在直接法的相位退火和切线扩展阶段(如PHAN和TREF指令中所指定)对其进行精修。不必为不同的相位集使用不同的初始相位，因为相位退火阶段本身引入(统计分布的)随机相移！对于部分结构的相位能力不太充分的情况，例如它只由一个原子构成时(例如大的有机结构中的P或S)，这是一种有效的部分结构扩展方法。若至少5个原子已经正确定位，则仅仅TEXP就足够了。

When  TEXP is used without TREF a tangent formula expansion (to all reflections  with E > Emin as specified on  the ESEL instruction) is first performed, followed by several cycles (see  FMAP) of E-Fouriers and peak-list  optimization. TEXP is particularly useful for cases in which several not very  heavy atoms (e.g. P, S) have been located by PATT followed by hand  interpretation of the resulting 'crossword table'. In such cases nH should be  set to the number of such atoms and na to about half the number of reflections  with E > 1.5 (see the first page of the SHELXS-96 output). ShelX-97 Manual

当使用TEXP而不使用TREF时，首先执行切线公式扩展(对ESEL指令中指定的E >  Emin的所有衍射点)，然后执行数轮(见FMAP)E傅里叶和峰列表优化。TEXP特别适用于已经由PATT定位了数个不太重的原子(例如P、S)，然后手工演绎产生的"纵横字谜表"的情况。在这种情况下，nH应当设置为与这种原子的数目相同的数字，na应当设为E >  1.5的衍射点数目的一半(见SHELXS-96输出的第一页)。ShelX-97手册

TREF和ESEL同ShelXS-DirectMethods，见上文。

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