Help Index
SAPI  for Microsoft Windows 95/98 and NT

Main authors:     Zheng Chao-de, Gu Yuan-xin, Wan Zheng-hua² and Fan Hai-fu

Institute of Physics, Chinese Academy of Sciences, Beijing 100080, China

___________________________________________________________________

Contents

1.	Introduction

2.	Getting started

3.	Running a job

4.	Data file and keyword file

5.	Solving crystal structures

6.	Locating heavy atoms in protein crystals

7.	What to do when you failed

8.	Keywords

9.	Index for keywords

10.	Use of menu


Introduction
1.  Introduction

The name SAPI is an abbreviation of "Structure Analysis Programs with Intelligent control". It may also be read inversely as "Institute of Physics, Academia Sinica".

SAPI is a program system for solving single crystal structures from X-ray diffraction data.

The complete system is made up of the following:

"SAPI"	Program and file manager of the SAPI system.

"PREPARE"	Program for preliminary processing of diffraction data.

"PHASE"	Program for direct phasing of diffraction data.

"EXFFT"	Program for the calculation of Patterson, Fourier and E-maps.

"SEARCH"	Program for the interpretation of results from "EXFFT".

"MODEL"	Program for editing structure models.

The second to fifth parts of SAPI is based on MULTAN [1] and differs from which by the following:

1. The program can automatically handle diffraction data of a structure having pseudo-translational symmetry and lead directly to the correct solution in favorable cases. This is particularly useful for solving superstructures without relying on assuming a structure model.

2. The program can recognize pseudo-centrosymmetric solutions when dealing with non-centrosymmetric structures. In addition, the program can break the enantiomorphous ambiguity given the "atomic positions" of both enantiomorphs.

3. Instead of the phase permutation, random starting phases are assigned to a large starting set, which can include all reflections except the origin and enantiomorph fixing reflections. By default, 250 reflections are used.

4. The program possesses the ability of intelligent control on the path of phase development according to the feature and complexity of the structure.

5. The programs EXFFT and SEARCH of MULTAN have been modified to include the calculation and peak search for Patterson and Patterson-superposition functions. This enables the effective combination of Patterson and direct methods. Besides, a full automatic procedure is provided for Patterson analysis of structures containing heavy atoms.

6. The program for the interpretation of space group symbols written by Burzlaff and Hountas [2] has been modified and included.

Many crystal structures can easily be solved by one of crystal-structure solving packages known on the world. However there are still some structures which resist solution. In fact, most of the "difficult structures" have some kind of pseudo symmetry. One of the typical features of SAPI is that it provides facilities for solving problems arising from various kinds of pseudo symmetry. For the theoretical background on the treatment of pseudo symmetry, the reader is referred to Fan Hai-fu & Zheng Qi-tai [3], Fan Hai-fu [4] and the references there in. For details of the random-starting-phases procedure used in SAPI, see Yao Jia-xing [5]. Some special applications of SAPI are described in detail by Fan et al. [6]-[8].

The authors should like to express their gratitude to Professor M. M. Woolfson for helpful discussions and encouragement with this project. The authors would like to thank Dr. P. Main for his help with MULTAN. Thanks are also due to Professor Zheng Qi-tai, Dr. Yao Jia-xing, Dr. Han Fu-son and Dr. Yu Zhao-xian, who helped in many ways.

References

[1] P. Main, S.J. Fiske, S.E. Hull, L. Lessinger, G. Germain, J.P. Declercq & M.M. Woolfson (1980). MULTAN-80: A System of Computer Programs for the Automatic Solution of Crystal Structures from X-ray Diffraction Data. Univs. of York, England and Louvain, Belgium.

[2] H. Burzlaff & A. Hountas (1982). J. appl. Cryst. 15, 464-467.

[3] Fan Hai-fu & Zheng Qi-tai (1982). Acta Phys. Sin. 31, 191-198. (in Chinese)

[4] Fan Hai-fu (1984). Rigaku Journal Vol.1 No.2, 15-21.

[5] Yao Jia-xing (1981). Acta Cryst. A37, 642-644.

[6] Fan Hai-fu, Yao Jia-xing & Qian Jin-zi (1988). Acta Cryst. A44, 688-691.

[7] Fan Hai-fu, Qian Jin-zi, Yao Jia-xing, Zheng Chao-de & Hao Quan (1988). Acta Cryst. A44, 691-692.

[8] Fan Hai-fu, Qian Jin-zi, Zheng Chao-de, Gu Yuan-xin, Ke Heng-ming & Huang Sheng-hua (1990). Acta Cryst. A46, 99-103.


Getting started
2.  Getting started

1. Load the whole package into a separate directory, say C:\SAPI.

2. Drag and drop SAPI.EXE into an existing program group of the Program Manager of Windows 3.1. Or, the user can create a new program group and put SAPI.EXE as well as MODEL.EXE in it.

3. To invoke SAPI, the user would double click SAPI.EXE from the File Manager or double click the corresponding icon from the Program Manager.


Running a job
3.  Running a job

1. Before running SAPI to solve a crystal structure, it is necessary to prepare for the crystal a data file and a keyword file. The former contains diffraction data from the crystal, while the latter contains the corresponding crystallographic parameters and keywords needed for the job control. Details of these files are given in next section: "Data file and keyword file".

2. If it is the first time that SAPI is used to solve the crystal structure, you would first prepare a data file containing the diffraction data. Then you would invoke SAPI as described in the previous section: "Getting started". From the "File" menu click the item "New keyword file", a dialog box will appear. After entering some necessary information in it, SAPI will create the keyword file and display it on the screen. Finally from the "File" menu click the item "Run", SAPI will then start running in the default direct method mode.

3. If you have already both data file and keyword file in your hard disk, to start a job, you would first invoke SAPI, open the keyword file by using "Open" from the "File" menu and then select "Run".

4. If you would like to run SAPI in a way other than the default, SAPI provides nearly a hundred of Keywords, which could be used to change the mode of control. You could modify a keyword file using a text editor if you are familiar with the keywords. However it is more convenient to use the menus provided in SAPI. To do this, first invoke SAPI. Open an existent keyword file or create a new keyword file. Then from the "Jobs" menu select one of the items under the title "Set options:". By following the instructions given in a number of dialog boxes, a modified keyword file will be create automatically.

5. Upon completion of a SAPI job, a graphical representation of the resultant map and a summarized text output will be displayed on the screen by the program MODEL. Each SAPI job produces a number of files having a common root of filename and different extensions. For example, a direct-method job run with the data file "CORT_.HKL" and the keyword file "CTSN.D01" yields the following output files:

CORT_D01.OUT	a text file containing the output and a copy of the keyword file.
CORT_D01.SUM	a summary of CORT_D01.OUT to be read by MODEL.
CORT_D01.PLT	a text file to be read by MODEL for structure-model editing.
CORT_D01.PKS	a text file containing the peak list to be used in further calculations.
CORT_D01.MAP	a binary file containing the E-map to be used in further calculations.

6. The program MODEL for structure-model editing can run independently. It reads *.PLT and *.SUM files and produces *.SCF and *.ATM files. The *.SCF files are in the "standard crystallographic file structure-90" format and are used by MODEL as default input files. The *.ATM files contain the atom list to be used in further calculations. MODEL can be call either from MS Windows or from SAPI:

from MS Windows: double click MODEL.EXE from the file manager or double click the corresponding icon from the program manager;

from SAPI: open a *.PLT or *.SCF file from the "File" menu or select "Edit models" from the "Jobs" menu.


Data file and keyword file
4.  Data file and keyword file

The user should prepare two files before running SAPI: the data file and the keyword file. The former contains the diffraction data while the latter consists of the necessary crystallographic information and some controlling parameters. Both files are to be read by the program "PREPARE".

4.1   The data file

4.2   The keyword file


The data file
4.1  The data file

This file should contain a record specifying the run time format, followed by records of reflections with H, K, L, F(obs) and ID, where all are integer except F(obs). ID=0 for observed reflections, ID=1 for unobserved. the program will not allow unobserved reflections to be used in phase determination no matter how large the E-value. Owing to the reason of packing the maximum magnitude of H, K or L is 128. The data are terminated with a dummy reflection with negative F(obs). The program expects a complete set of reflections (observed and unobserved) of unique reflections (those not related by symmetry). Failure to observe these points will result in inaccurate calculation of the E's. On the other hand, The program will reject the systematically absent reflections (caused by screw axes, glide planes, and lattice centrings) according to the given space-group sysmmetry.

The user can also put any number of comment lines (records) on the top of the data file. It is recommended not to use pairs of parentheses, " (" and ")", within a comment line, otherwise the record should contain at least one character other than those of the following:

1234567890., ()FHIX

An example of data file is given below:

File name:       hwhk.hkl                      ; begin of data file

Compound name:   huangheite

Space group:     R 3

Cell parameters: a=5.070 c=38.408 gamma=120 Z=6

Cell contents:   C 12   O 36  F 6   Ba 12

(3I3,F6.2,I2)

0  0  6 11.40 0

0  0  9 23.62 0

0  0 12 81.03 0

0  0 15 65.75 0

      .

      .

      .

5  0 11  5.08 0

6 -3 -3  4.58 1

6 -3  0 53.85 0

6 -3  3  4.12 1

      .

      .

      .

5  0 16 -5.08 0     ; dummy reflection, end of data file.


The keyword file
4.2  The keyword file

A keyword command in the keyword file can be written in one or more records, each of which should not exceeds 80 characters. The Keyword file should begin with a title record and end with the keyword END. A typical keyword file is like the following.

* * * *   Cortisone   C21 H28 O5   Z=4   * * * *

CONTENTS-UNIT-CELL	C   84   H  112   O   20

CELL-DIMENSIONS	10.0400   23.6490   7.7840    90.000    90.000    90.000

SPACE-GROUP	P 21 21 21

DATA-FILE-HKL	e:\sapi\samples\cort\cort.HKL

END

A full description of all available keywords is given in paragraph 8. Keywords


Solving crystal structures
5.  Solving crystal structures

In the following we provide a number of examples of different complexity. Some of them were solved by a default run of SAPI, others by using SAPI in a special way. Detailed results of each example are stored in a separate sub-directory. For example, results of "Cortisone" can be found in the sub-directory ...SAPI\SAMPLES\CORT. Note that owing to a small change of the temperature and scaling factors some results here may be slightly different with that previously published.

5.1   Ordinary structures

5.2   Structures with pseudo-translational symmetry

5.3   Structures with pseudo-centrosymmetry


Ordinary structures
5.1  Ordinary structures

Examples:

1.   Cortisone

2.   BZ1

3.   SZCJ


Cortisone

Space group: P 21 21 21

Cell dimensions: a=10.040, b=23.649, c=7.784Å

Cell contents: C84 H112 O20

Files: ...SAPI\SAMPLES\CORT\*.*

This is a typical organic structure consists of light atoms. A default run of SAPI in direct-method mode revealed 25 out of the total 26 independent non-hydrogen atoms. Two cycles of Fourier iteration led to the complete structure with an R factor of 21.9.


BZ1

Space group: P 21

Cell dimensions: a=10.044, b=15.524, c=16.333Å; ß=107.35°

Cell contents: C82 H98 O38 N2

Files: ...SAPI\SAMPLES\BZ1\*.*

This is a "light-atom" organic structure of moderate complexity. A default direct-method run yielded only a fragment of the molecule. However, the Karle recycling based on it revealed the main part of the structure. 4 cycles of Fourier iteration brought out all the independent non-hydrogen atoms. During the direct-method run of this example, the weighting scheme of tangent refinement changed automatically by the program from the conventional weighting to statistical weighting. This improved the result of the direct method. It was also seen that the Karle recycling gave better result (see BZ1-KAR.SCF) than that of Fourier synthesis (see BZ1-F00.SCF), when the known part is not sufficient to dominate the phases. Results of direct methods are in files BZ1-D01.*, results of Karle recycling are in files BZ1-KAR.*, while results of Fourier iteration based on the Karle recycling are in files BZ1-F01.* to BZ1-F05.*.


SZCJ

Space group: P 21 21 21

Cell dimensions: a=11.5, b=8.8, c=16.5Å

Cell contents: C56 N8 Br4 H84 O8

Files: ...SAPI\SAMPLES\SZCJ\*.*

This example shows how Patterson method can help with solving a structure containing heavy atoms. A default run of SAPI in direct-method mode did not reveal the main feature of the structure (see SZCJDR1.SCF). However a default run of Patterson Analysis let to the whole structure (see SZCJAPA.SCF).


Structures with pseudo-translational symmetry
5.2  Structures with pseudo-translational symmetry

In the following, all the sample structures possess some kind of pseudo-translational symmetry, they are difficult to solve by conventional direct methods or Patterson methods. However they could be easily solved by SAPI, since SAPI provides facilities for dealing with such kind of problems. For a better understanding of the material, readers are referred to reference [4] cited in paragraph 1: "Introduction"

Examples:

1.   Freielebenite

2.  Hwangheite

3.   PTS6

4.   PTS24

5.   Wwz


Freielebenite(Ito & Nowacki, 1974)
Freielebenite

Space group: P 21/a

Cell dimensions: a=7.518, b=12.809, c=5.940 Å; ß=92.25°

Cell contents: Pb4 Ag4 Sb4 S12

Files: ...SAPI\SAMPLES\FREI\*.*

This is a typical superstructure and had been a test structure of the key shift method (T. Ito, (1973). Z. Krist. 137, 399-411). There are two pseudo-translation vectors t1 = a/2 and t2 = b/3 in the unit cell. The asymmetric unit contains only six atoms. However Patterson and conventional direct methods did not lead to the correct structure. The true structure differs from the average one by small shifts of atomic positions with respect to those of the average structure. A default run of SAPI indicated that the structure possesses pseudo-translational symmetry. The reflections were classified automatically by the program into six index groups and normalized separately. Phase derivation resulted in an E-map, of which the top six peaks correspond to the six independent atoms with 17 of the total 18 positional shifts consistent with those obtained by Ito. The structure model so obtained gives an overall R-factor of 31.83. Two cycles of Fourier iteration brought the R-factor down to 12.70. For crystal structures having pseudo-translational symmetry, it is useful to have R-factors calculated separately for reflection groups divided according to the pseudo-translational symmetry. SAPI provides such kind of R-factors in Fourier calculations. The user should specify how to divide reflections in groups using the keywords NR-GROUPS-SPECIFIED and GROUP-HKL. Results for the present example are listed below.

Group	R-factors
	Model from the  direct method	Model after Fourier iteration
______________________________________________________________

1.     h = 2n;         k = 3n	22.96	6.71
2.     h = 2n;         k = 3n + 1	33.79	15.79
3.     h = 2n;         k = 3n + 2	28.63	17.43
4.     h = 2n + 1;   k = 3n	66.89	24.52
5.     h = 2n + 1;   k = 3n + 1	43.02	17.20
6.     h = 2n + 1;   k = 3n + 2	28.39	13.63
______________________________________________________________

All reflections	31.83	12.70


Hwangheite

Space group: R 3

Cell dimensions: a=5.070, c=38.408 Å; gamma=120°

Cell contents: Ba6 Ce6 F6 C12 O12

Files: ...SAPI\SAMPLES\HWHK\*.*

This is a superstructure with 14 atoms in the asymmetry unit. There are two independent Ba atoms respectively close to (0,0,0) and (0,0,1/2) and two Ce atoms respectively close to (0,0,1/4) and (0,0,3/4). Hence there is a pseudo-translation vector t = c/4 in the unit cell. Patterson and conventional direct methods failed to solve the true structure, since they could not find the positional shifts of Ba and Ce atoms correctly. A Fourier map phased with the average positions of Ba and Ce atoms  yields eight rather than two independent F atoms and six instead of three O atoms for each CO3 group. This makes the structure analysis rather complicated. However a default run of SAPI resulted in an E-map, on which the largest four peaks correspond to the four heavy atoms with correct positional shifts. Fourier synthesis phased by the four heavy atoms revealed the complete structure. R-factors calculated from the four heavy atoms and from the structure model obtained after one cycle of Fourier iteration are list below.

Group	R-factors
	Heavy atoms from the direct method	Model after  Fourier synthesis
______________________________________________________________

1.     l = 4n	14.29	4.63
2.     l = 4n + 1	29.17	16.33
3.     l = 4n + 2	56.87	43.96
4.     l = 4n + 3	31.42	17.83
______________________________________________________________

All reflections	28.49	11.97


PTS6

Space group: P 21/c

Cell dimensions: a=24.420, b=8.363, c=24.747Å; ß=90.22°

Cell contents: C216 H248 N8 O72

Files: ...SAPI\SAMPLES\PTS6\*.*

This is an organic structure which failed to solve by conventional methods and was for the first time solved by SAPI. The structure consists of light atoms and possesses a pseudo-translation vector, t = (a + c)/2 . A default run of SAPI in direct-method mode revealed almost the complete structure which includes two independent molecules related by the pseudo-translation vector.


PTS24

Space group: P 21

Cell dimensions: a=12.486, b=10.822, c=14.609 Å; ß=109°

Cell contents: C72 H72 O12 N4 Br4

Files: ...SAPI\SAMPLES\PTS24\*.*

The structure resisted solving by conventional methods. It contains a pseudo-translation vector t = b/2 + c/2 , which relates two independent molecules in the asymmetric unit. Even more the chemical formula of the unit cell is not certain before the complete structure was solved by SAPI. The E-map resulted from a default run of SAPI failed to reveal the skeleton of the molecules. However four cycles of Fourier iteration started from the top 28 peaks on the E-map led finally to the complete structure, which consists of two independent organic molecules and three independent water molecules. Each of the organic molecules contains one more non-hydrogen atom than the original chemical formula shows.


Wwz

Space group: P 21 21 21

Cell dimensions: a=19.253, b=15.992, c=7.280 Å

Cell contents: C92 H108 O28 Br4

Files: ...SAPI\SAMPLES\Wwz\*.*

The structure resisted solving by conventional methods. The 4 Br atoms in the unit cell are related by a pseudo-translation vector t = a/2 + c/2 and a pseudo inverse center at (1/4, 0, 0). The E-map resulted from a default run of SAPI failed to reveal the skeleton of the molecules. However a superposition of the E-map with the Patterson map at the positions of Br atoms ( using the keyword MIN-EMAP-PATTERSON) revealed the essential feature of the structure.


Structures with pseudo-centrosymmetry
5.3  Structures with pseudo-centrosymmetry

In the following, an example is given which possess pseudo-centrosymmetry. The structure is difficult to solve by conventional direct methods or Patterson methods. For a better understanding of the theory involved, readers are referred to reference [4] cited in paragraph 1. "Introduction".

Examples:

1.   ZCW


ZCW

Space group: P 21

Cell dimensions: a=12.58, b=14.38, c=11.00 Å; ß=114.6°

Cell contents: C68 H96 N2 O22 I2

Files: ...SAPI\SAMPLES\ZCW\*.*

The unit cell contains two iodine atoms in centric arrangement giving rise to a problem of enantiomorphous ambiguity. Either Patterson or direct methods resulted in a pseudo centric map containing simultaneously the true structure and its enantiomorph. Except for the iodine atom, it is difficult to recognize the true atom from each pair of centrosymmetrically related peaks. The structure can be solved by the following procedure:

1) Run SAPI in the mode of Automatic Patterson Analysis to obtain a pseudo centric map, the position of the pseudo inverse center is 0.0, 0.25, 0.0 in this case (see ZCW-P01.SCF). Since both enantiomorphs will appear on the map, no interpretation is needed in this stage and the number of peaks required on the output list should be more than twice of the number of independent atoms. For this purpose the keywords "NO-JOIN" and "NR-PEAKS-TO-LIST        100" are included in the keyword file (ZCW-.P01). This can be done easily by using the SAPI menu.

2) Select "Solving Enantiomorph Ambiguity" from the "Direct methods" sub-menu in "Set options:" of the "Jobs" menu. The menu driver will help you to put into the keyword file (ZCW-.DP1) the peak list of ZCW-P01.PKS. The keyword file is edited further as follows:

a) Assign the largest peak as iodine with occupancy equal to 1.0.

b) Delete all the peaks lying on or close to the pseudo mirror plane, i.e. to delete those peaks with their y coordinate within 0.05 apart from that of the pseudo mirror plane. The position of the pseudo mirror plane are y=0.0 and 0.5 in this case.

c) Assign 40 (approximately the number of independent light atoms) pairs of the remaining peaks as carbon atoms with occupancy equal to 0.5. Alternatively, we can assign the occupancy of the iodine atom as 2 and assign that of the remaining atoms to 1. The program was then run in a special direct method mode (for the results see ZCW-DP1.SCF).

3) Four cycles of Fourier calculation based on the result of 2 leads to the complete structure, see ZCW-F04.SCF.


Locating heavy atoms in proteins
6.  Locating heavy atoms in proteins

SAPI can be used to determine heavy-atom sites in protein structures by either direct methods or Patterson methods with either single isomorphous replacement (SIR) or one wave length anomalous scattering (OAS) data. In the SIR case, the absolute values of the difference between the structure-factor magnitudes of the native protein and the heavy-atom derivative should be used as input F(obs). While in the (OAS) case, the absolute difference of the structure factor magnitudes of the Friedel pairs should be used. In case that there are more than one independent heavy atom in the unit cell and some of them are in known positions, then the positions can be used in the calculation of normalized structure factors by using the keyword CLUSTER-POSITIONED. This is sometimes helpful for locating the remaining heavy atoms.


What to do when you failed
7.  What to do when you failed

Some of the suggestions given in the user's manual of MULTAN-80 are also included in the following.

7.1   Make sure every thing input to the program is correct

7.2   Check if there is something abnormal

7.3   Try more

7.4   Make use of partial structural information

7.5   Change something

7.6   Contact the authors


Make sure every thing input to the program is correct
7.1  Make sure every thing input to the program is correct

If there are several possible space groups, try the one with lowest symmetry first. For some difficult structures, better result may be obtained by replacing the space group with one of its sub-groups.


Check if there is something abnormal
7.2  Check if there is something abnormal

1. Check the distribution of average E**2 with Sin(theta). If the average E**2 at high angles are too large (> 1.0) it may be necessary to renormalise using a smaller temperature factor. Besides, a smaller temperature factor is also recommended to use when there are a few outstanding large E's at high angle range. An alternative way to treat with this case is to set a maximum limit of Sin(theta), using the keyword RHO-MAX or LIMIT-RESOLUTION.

2. Check the print out of auto-grouping of reflections to see whether there is another reasonable way to divide reflections in groups. For a difficult structure with pseudo-translational symmetry, it would be better to try all possible way on grouping the reflections for normalization.

3. If there are too few phase relationships per reflection and there is room for more relationships in the computer, increase the number of reflections. If there are already too many relationships for the computer to hold, decrease the number of reflections to the point where most of the relationships set up can be held in store.

4. If the phase relationships conflict too much with each other (abnormally small absolute figures of merit may result in this case), decrease the number of reflections may give better result.

5. For difficult structures where there is a paucity of relationships, it may be necessary to use the relationships with a kappa value less than 0.6. In this case it is usually best to use all the relationships (use the keyword " KAPPA-MIN      0").

6. If the early figures of merit are rejecting most of the sets, it may be possible that they are rejecting the correct set too. If you believe that this is happening, do not use them. For planar ring

structures, remember to switch off the first EARLY-FOM using " CUT-A-EARLY-FOM      0" and raise the limit on the second EARLY-FOM, e.g. "CUT-B-EARLY-FOM      1.7".

7. For a difficult structure, the combined figure of merit may not indicate the "correct" set of phases very reliably. Be sure to examine E-maps further down the ranking order than is usually necessary.


Try more
7.3  Try more

One of the hints on using random-starting phasing procedures is to try more whenever you failed. There have been some difficult structures, which resist solution by a default run of SAPI in direct-method mode. However they can be solve easily within a thousand random trials.


Make use of partial structural information
7.4  Make use of partial structural information

1. As a matter of fact, an "uninterpretable" E-map is not necessary an incorrect E-map. Fourier or Karle recycling starting from the top part of the peak list often lead to the complete structure. Alternatively MIN-EMAP-PATTERSON, the superposition of E-map and Patterson map, can also be helpful. For Fourier recycling, the known part should usually be able to contribute more than one half of the total scattering power of the whole unit cell. To start with a smaller fragment, KARLE-RECYCLING would better be used instead. On the other hand, if a starting atomic group failed to develop the remaining part of the structure, try to use a smaller or larger starting group. This may often give better result. In the final stage of Fourier recycling, it is recommended to use uniform weight WEIGHT-UNITY instead of Sim weight. This will result in a larger difference of peak height between true atoms and ghost peaks.

2. A common incorrect solution is a correct oriented molecular fragment misplaced with respect to the symmetry elements. such fragments can be input to PREPARE for use in the normalization.

3. If the user believes that a few largest peaks on the E-map are true atoms but they are not enough to develop the whole structure by usual way, then a Patterson superposition MIN-PATTERSONS based on these peaks is recommended.


Change something
7.5  Change something

Direct methods are sensitive to the values of E's and the controlling parameters. A small change lead often to a very different result. If you failed without knowing the reason, then just try to change something, such as the temperature factor, scaling factor, atomic scattering factor or other factors affecting E's. You may also try to change the weighting scheme for tangent refinement, the number of reflections used for phase derivation, the number of reflections in the starting set, the initial weight of the random starting phases, the minimum kappa value, ... etc.


Contact the authors
7.6  Contact the authors

When everything else has failed, the authors are usually willing either to discuss a particular structure or to attempt a solution of the structure themselves.


Use of menu
11.   Use of menu

Commands

File Menu

Edit Menu

Search Menu

Windows Menu

Toolbar

Toolbar Commands

Procedures

Copying Text

Deleting Text

Exiting

Edit Window

Drag/Drop from the File Manager

Printing

Keyboard Topics

Windows Key Strokes


For information on how to use Help, press F1 or select Using Help from the Help menu.


Edit Menu

The Edit menu provides commands to undo edits, access the clipboard, and to delete text.

Undo	Undo the previous operation.

Cut	Delete selected text and move it to the clipboard.

Copy	Copy selected text to the clipboard.

Paste	Move text from the clipboard to the current document.

Clear All	Delete all text in document.

Delete	Delete selected text.


File Menu

The File menu provides commands for creating new files, opening existing files, saving files, printing files, and exiting the application.

New	Create a new, untitled, document.

Open	Open an existing file.

Close	Close the current document.

Save	Save the current document if its contents have changed.

Save As	Save the current document under a new name.

Print	Print the current document.

Print Preview	View a sample printout of the current document.

Print Setup	Set printer characteristics.

Exit	Exit SAPI application.


Search Menu

The Search menu provides commands to find and replace text.

Find	Find a pattern of text.

Replace	Replace one pattern of text with another.

Next	Find and/or replace the next occurrence of text pattern.


Windows Menu
Window Menu

The Window menu provides commands to control the position and layout of application's windows.

Cascade	Resize and position all windows in an overlapping pattern.

Tile	Resize and position all windows in an non overlapping pattern.

Arrange Icons	Align all iconized windows along a grid.

Close All	Close all windows.


Copying Text

To copy text to a document from the clipboard, position the cursor at the desired insertion point, and choose Edit|Copy from the menu.


Deleting Text

To delete text from a document, select the text, and choose Edit|Cut or Edit|Delete from the menu. Cut will put the deleted text in the clipboard, and Delete will simply delete it.


Exiting

To exit the application, choose File|Exit from the menu.


Edit Window

The edit windows in this application allow reading, editing, printing and saving text files up to 64K characters in size.


Drag/Drop from the Program Manager
Drag/Drop from the File Manager

A file can be opened into an editor in the application by dragging the file from the File Manager, and dropping it on sapi's main window.


Printing

There are three commands on the File menu which support printing of documents from the application. File|Print Setup is used to select and configure a printer device. File|Print Preview displays a special preview window which shows how the document will appear when printed. File|Print causes the current document to be printed.


Edit Copy Command

The Edit|Copy command leaves the selected text intact and places an exact copy of it in the clipboard. To paste the copied text into another document, choose Edit|Paste.


Edit Cut Command

The Edit|Cut command removes the selected text from your document and places the text in the clipboard. Choose Edit|Paste to paste the cut text into another document. The text remains selected in the clipboard, and can be pasted multiple times.


Edit Paste Command

The Edit|Paste command inserts the text currently selected in the clipboard into the current window at the cursor position.


Edit Undo Command

The Edit|Undo command restores the file in the current window to the way it was before your most recent edit operation. Undo inserts any characters you deleted, deletes any characters you inserted, replaces any characters you overwrote, and moves your cursor back to a prior position.


Edit Clear All Command

The Edit|Clear All command deletes the entire contents of the current document. Use Edit|Undo to restore the contents.


Edit Delete Command

The Edit|Delete command deletes the currently selected text from the current document. The text is not placed in the clipboard. Use the Edit|Undo command to restore the text.


File Close Command

File|Close closes the currently active window.


File Exit Command

The File|Exit command exits sapi. If you've modified documents without saving, you'll be prompted to save before exiting.


File New Command

The File|New command opens a new, untitled document, and makes it the active window. The application prompts you to name untitled documents when they are closed.


File Open Command

The File|Open command displays the Open a File dialog box so you can select a file to load into a new document window. You can also create a new document by naming a file that doesn't currently exist.


File Print Command

The File|Print command prints the contents of the active window. Use File|Print Preview to see how the document will be laid out on printer pages. Use File|Print Setup to select a printer, and to set printer options.


File Print Preview Command

File|Print Preview opens a special window that shows how the active document will appear when printed. The preview window shows one or two pages of the active document as they would be laid out on printer pages. Controls on the window allow you to page through the pages of the document.


File Print Setup Command

The File|Printer Setup command displays the Printer Setup dialog box which allows you to select and configure the printer to be used to print documents in the application.


File Save Command

The File|Save command saves the document in the active window to disk. If the document is unnamed, the Save File As dialog box is displayed so you can name the file, and choose where it is to be saved.


File Save As Command

The File|Save As command allows you to save a document under an new name, or in a new location on disk. The command displays the Save File As dialog box. You can enter the new file name, including the drive and directory. All windows containing this file are updated with the new name. If you choose an existing file name, you are asked if you want to overwrite the existing file.


Search Find Command

The Search|Find command searches the current document for a text pattern. The command displays the Find dialog which controls the search process. Options in the dialog determine whether only whole words are to be matched, whether the case of characters is significant, and whether the search should be conducted forwards or backwards through the document. As each match is found, it is highlighted in the document.


Search Next Command

The Search|Next command repeats the last Find or Replace operation.


Search Replace Command

The Search|Replace command searches the current document for a text pattern, and replaces occurrences of the of the pattern with new text. The command displays the Replace dialog which controls the search/replace process. Options in the dialog determine whether only whole words are to be matched, and whether the case of characters is significant. The dialog is also used to specify the pattern to search for, and the text to replace occurrences with.


Windows Arrange Icons Command
Window Arrange Icons Command

The Window|Arrange Icons command arranges all iconized windows into rows along the bottom of the application's main window.


Windows Cascade Command
Window Cascade Command

The Window|Cascade command arranges all document windows from the top-left position of the application's main window so that the title bar of each is visible.


Windows Close All Command
Window Close All Command

The Window|Close All command closes all document windows open in the application.


Windows Tile Command
Window Tile Command

The Window|Tile command arranges all document windows side-by-side in a non-overlapping pattern.


Keywords
8. Keywords

The keyword file should begin with a Title and end with the keyword END. Other keywords may be given in any order, however it is recommended that the user keep to the order given in the following sections.

A keyword is composed of one or more (up to 3) segments separated by a hyphen "-", e.g.

CONTENTS-UNIT-CELL

Only the first two segments (CONTENTS and UNIT in the above example) are significant. A keyword as a whole word can be truncated and each segment can also be truncated separately until the keyword is confused with others. For example the above keyword can be truncated to any one of the following:

CON-UN-CEL

C-U-C

C-U

CONT

When there are any ambiguities, the program will prompt with the whole list of keywords and the user may pick up the correct one from it.

8.1   Title, REMARKS & END

8.2   Basic keywords for PREPARE

8.3   Keywords for using partial structure information in normalization

8.4   Keywords dealing with pseudo translational symmetry in normalization

8.5   Keywords for fragment development

8.6   Keywords for Pattersons

8.7   Keywords for direct methods

8.8   Keywords for map calculation and interpretation


Title, REMARKS & END
8.1   Title, REMARKS & END

Title

The first record (line) of a keyword file is treated as a free format title. The program will put the character string containing in this record to the central part of an 80 character array, which is printed at the head of a number of pages of output.

REMARKS

If the user has a lengthy description of the computing job and wishes to print it on the first page of the output, this description can be written in free format records and put under the record 'REMARKS n' where n is the number of records of the description (including blank lines).

END

A keyword file should be ended with a record containing only this keyword.


Basic keywords for PREPARE
8.2   Basic keywords for PREPARE

SPACE-GROUP

CELL-DIMENSIONS

CONTENTS-UNIT-CELL

DATA-FILE-HKL

FACTORS-ATOMIC

B-FACTOR

SCALE-GROUP

E-HKL-INPUT

K-CURVE

NR-POINTS-WILSON

LIMIT-RESOLUTION

RHO-MAX

MISSING-HKL

RESCALE-PARITY-GROUP

PR-FOBS-E

FAST-JOB

SKIP-PREPARE


SPACE-GROUP s
SPACE-GROUP

Space group specification. This keyword should followed by a space group symbol. Examples:

SPACE-GROUP	P 21

SPACE-GROUP	P 21/A

SPACE-GROUP	P 21 21 21

SPACE-GROUP	P 43 21 2

SPACE-GROUP	P 63/M C M

SPACE-GROUP	F -4 3 M


CELL-DIMENSIONS a b c
CELL-DIMENSIONS     a b c alpha beta gamma

Cell dimensions. a, b and c are in angstroms. alpha, beta and gamma are in degrees. e.g.

CELL-DIMENSIONS    10.040   23.649   7.784   90.0   90.0   90.0


CONTENTS-UNIT-CELL     c1  n1  c2  n2  c3  n3  .........

Unit cell contents. c1 is the chemical symbol of atomic type 1, n1 is the number of atoms of this type in the unit cell etc. to a maximum of 8 atomic types. e.g.

CONTENTS-UNIT-CELL     C  20    H  34    S  1

Input the total contents of the unit cell - include all atoms whether the lattice is centred or primitive. Include all  atoms whether input later as part of a group or not. Include all atoms whether their scattering factors are already stored in the program or not. Scattering factors for neutral atoms with atomic number from 1 to 98 are stored in the program.

If an atom in the unit cell is not one of the above, the constants for the analytical scattering factor should be input using the keyword FACTORS-ATOMIC.

When the keyword 'CONTENTS-UNIT-CELL' is omitted, the program will calculate the number of atoms in the unit cell by assuming that there are only carbon atoms in the unit cell and that the density of the crystal is 1.2 g/cm³ .


DATA-FILE-HKL

This keyword specifies the path and filename of the data file which contains the whole set of diffraction data to be used for crystal-structure analysis.

Example:

DATA-FILE-HKL           e:\sapi\samples\cort\cort.hkl


FACTORS-ATOMIC     c1  a  a'  b  b'  c

FACTORS-ATOMIC     c1  a  a'  b  b'  c  c'  d  d'  e

Analytical scattering factor constants for atomic type c1. The scattering factor curve is represented as:

f = a*exp(-a'*S²) + b*exp(-b'*S²) + c

or

f = a*exp(-a'*S²) + b*exp(-b'*S²) + c*exp(-c'*S²) + d*exp(-d'*S²) + e

Where S = sin(theta)/lambda. For  values of five constants per atom see Forsyth and Wells, Acta Cryst. 12 (1959) 412. For values of nine constants per atom see "International Tables for X-ray crystallography" Volume IV.


B-FACTOR     X1 X2 X3 ..... X8

SCALE-GROUP     X1 X2 X3 ..... X8

The user can specify temperature(B) and scaling(K) factors for up to 8 different index groups.

SQRT(K)*F(obs) = exp(-B)*F(cal)

If only X1 is specified, the  value will be used for all reflections. If only the temperature factors are specified, the program will calculate the corresponding scaling factors. However scaling factors can not be specified without the corresponding temperature factors.

When using SAPI for Fourier recycling, B-FACTOR must be specified or the resulting R-factors will be meaningless.


E-HKL-INPUT

E values instead of F(obs) are used as input data to the program "PREPARE".


K-CURVE

If specified, the F(obs) will be normalized by a K-curve interpolation. The default is that the F(obs) will be normalized by a least-squares straight line through the Debye (or Wilson) curve.


NR-POINTS-WILSON     n

Specify the number 'n' of points on Wilson plot.


LIMIT-RESOLUTION     x

Resolution limit (in angstroms) set for reflections to be accepted in progams "PHASE" and "EXFFT". The default is that all the data will be used.


RHO-MAX     x

Maximum  value of (sin(theta)/lambda)² accepted for reflections to be transferred to programs "PHASE" and "EXFFT". The default is that all the data are to be accepted.


MISSING-HKL

In protein diffraction data, large number of weak reflections might be missing. This leads sometimes to large error in Wilson statistics. The keyword MISSING-HKL is used to compensate this effect.


RESCALE-PARITY-GROUP

If specified, different scaling factors will be applied to different index groups. The default is that an overall scaling factor will be used, provided no pseudo-systematic-extinction is found by the program.


PR-FOBS-E

Produce a complete list of F(obs) and E's. The default is no listing for the F(obs) data.


FAST-JOB

Fast implementation, in which the subroutine "AUTOGP" will be by-passed. This keyword also affects the path of the program "PHASE". It implies that the earlyfigure of merit with floatable cutoff is to be used.


SKIP-PREPARE

By-pass the program "PREPARE" after keywords have been input.


Keywords for using partial structure information in normalization
8.3   Keywords for using partial structure information in normalization

It is possible to input atomic groups of known geometry to "PREPARE" to improve the normalization either by the Debye curve or K-curve method.

CLUSTER-RANDOM

NR-CLUSTER-RANDOM

CELL-CLUSTER

CLUSTER-ORIENTED

CLUSTER-POSITIONED


CLUSTER-RANDOM

This keyword heads atomic parameters referring to a randomly oriented and randomly positioned cluster.


NR-CLUSTER-RANDOM     x

Number of times the random cluster appears in the unit cell.


CELL-CLUSTER a b c
CELL-CLUSTER     a b c alpha beta gamma

The cell to which atomic parameters of a random cluster are referred. The default is an orthogonal system with a = b = c = 1.0 angstrom, alpha = beta = gamma = 90 degrees.


CLUSTER-ORIENTED

This keyword heads atomic parameters referring to a correctly oriented but randomly positioned cluster.


POSITIONED
CLUSTER-POSITIONED

This keyword heads atomic parameters referring to a correctly positioned cluster.


Keywords dealing with pseudo translational symmetry in normalization
8.4   Keywords dealing with pseudo translational symmetry in normalization

WILSON-GROUP

NR-GROUPS-SPECIFIED

GROUP-HKL

E-SQUARE-MAX

RATIO-ST-TL

NO-AUTOGP


WILSON-GROUP

Wilson statistics will be applied separately to each parity group defined by the program or to each specified index group defined by the user. Individual temperature factor and scaling factor for each group will be calculated.


RESCALE-SPECIAL-GROUP m
NR-GROUPS-SPECIFIED     m

Reflections will be divided into m ( <= 8) groups according to the index relations specified by the keyword GROUP-HKL.


GROUP-HKL     n p1H+p2K+p3L=p4N+p5; p6H+p7K+p8L=p9N+p10; p11H+p12K+p13L=p14N+p15

Where p1, p2, ... ,p15 are integer coefficients. This keyword is used with the keyword NR-GROUPS-SPECIFIED. It specifies index relationships for the nth reflection group. In the above relations, any coefficient preceding the character H, K, L or N may be omitted if it equals 1; any term may be entirely omitted if the corresponding coefficient equals zero; any relation may be omitted if the right-hand side of the equation equals N. The arithmetic operator  '+'  between two terms may be replaced by  '-'  if necessary. In addition, one or more blank spaces may be used instead of a semicolon or be inserted in front or behind of any expression.

Example 1:

NR-GROUPS-SPECIFIED     4

GROUP-HKL     1     H+K=2N;     K+L=2N

GROUP-HKL     2     H+K=2N;     K+L=2N+1

GROUP-HKL     3     H+K=2N+1;     K+L=2N

GROUP-HKL     4     H+K=2N+1;     K+L=2N+1

Note that the last record 'GROUP-HKL     4 ... ' may be omitted without affecting the grouping condition.

Example 2:

NR-GROUPS-SPECIFIED     4

GROUP-HKL     1     L = 4N

GROUP-HKL     2     L = 4N+1

GROUP-HKL     3     L = 4N+2

Example 3:

NR-GROUPS-SPECIFIED     2

GROUP-HKL     1     H+K+L=4N

This example implies that group 2 will include all the reflections with H+K+L not equal to 4N.

Example 4:

NR-GROUPS-SPECIFIED 2

GROUP-HKL 1 H=4N

GROUP-HKL 2 H=4N+1

This example implies that all the reflections with H equal to 4N+2 or 4n+3 will be rejected.

If both NR-GROUPS-SPECIFIED and GROUP-HKL are not specified, the program can divide reflections into groups automatically in a proper way taking account of the statistic distribution of reflection intensities.


E-SQUARE-MAX     x

Those index groups with averaged E² less than x will be treated by the program as index groups having intensities systematically weak. The default value is 0.50. Once systematically weak reflec-tion group(s) have been found, the program will try to solve the translational ambiguity automatically.


RATIO-ST-WK x
RATIO-ST-TL     x

Specify the ratio x between the number of 'systematically strong' reflections and that of the total reflections to be passed to the program "PHASE". This keyword has effect only if the crystal possesses some kind of pseudo-translational symmetry and the reflections are divided into 'systematically strong' and 'systematically weak' groups. The default is x = (number of 'strong' groups)/(number of total groups). If x is given a value greater than 1, it means that there will be no restriction on the ratio.


NO-AUTOGP

By-pass the subroutine "AUTOGP". If not specified and if there is no any of the keywords WILSON-GROUP, NR-GROUPS-SPECIFIED, B-FACTOR and SCALE-GROUP in the keyword file, the program will scan the E values and search for pseudo-systematic extinction. Once this is found, the reflections will be grouped automatically according to the pseudo-systematic-extinction rule.


Keywords for fragment development
8.5   Keywords for fragment development

KARLE-RECYCLING

FOURIER-WEIGHTED

FOURIER-DIFFERENCE

WEIGHT-UNITY

SOLVE-ENANTIOMORPH

Atomic parameter specification


KARLE-RECYCLING n
KARLE-RECYCLING

This keyword heads atomic parameters for multi-solution Karle recycling. Apart from those known phases determined by the partial structure, 250 reflections having randomly assigned phases with initial weight equal to 0.45 are added to the starting set. Statistically weighted tangent refinement is used as default for both cases. If the user wants to change the number of random starting phases, or the initial weight of random phases, or the weighting scheme for the tangent refinement, the corresponding keyword(s) should be added after the keyword KARLE-RECYCLING.


FOURIER-WEIGHTED

This keyword heads atomic parameters for Fourier recycling with the Sim distribution as a weight function. The ' B-FACTOR' or the thermal parameters for individual atoms should be specified otherwise the resultant R-factors will be meaningless.


FOURIER-DIFFERENCE

This keyword heads atomic parameters for difference Fourier recycling with the Sim distribution as a weight function. The ' B-FACTOR' or the thermal parameters for individual atoms should be specified otherwise the resultant R-factors will be meaningless.


WEIGHT-UNITY

When this keyword is specified together with FOURIER-WEIGHTED or FOURIER-DIFFERENCE, unit weight will be applied instead of the Sim weight.


SOLVE-ENANTIOMORPH     x y z

Solve the enantiomorphous ambiguity. Where x y and z are the position parameters of the pseudo-inverse centre. If x y and z are not specified, the default will be (0,0,0). This keyword heads atomic parameters referring to a group consists of both enantiomorphs with the occupancy of each 'atom' equal to 0.5. Alternatively the group can also consists of atoms with their occupancy equal to 1, each of which comes from either one of the two enantiomorphs. The program will first result in an E-map with different peak heights for the two enantiomorphs. Then for each pair of enantiomorphs the one with lower peak height will be rejected from the output list. If the resultant map is not 'clean' enough for solving the structure, it is recommended to calculate a minimum function by using the keyword MIN-EMAP-PATTERSON.


Atomic parameter-specification
Atomic parameter specification

c1 x1 y1 z1 n1 q1 u11(1) u22(1) u33(1) u23(1) u13(1) u12(1)

c2 x2 y2 z2 n2 q2 u11(2) u22(2) u33(2) u23(2) u13(2) u12(2)

.

.

.

c1  is  the  symbol  of  the 1st atom. The symbol must be one of those specified in CONTENTS-UNIT-CELL.  x1, y1 and z1 are coordinates of the 1st atom. The following parameters are optional:

n is the code number of atom. q is the occupancy. u's are the anisotropic thermal parameters. u*8(pi)² = B. If only u11 is given, the program will treat it as isotropic temperature factor. The code number has no effect in the calculation. It is not allowed to omit any of the optional parameters if after which one or more parameters belonging to the same atom are given.


Keywords for Pattersons
8.6   Keywords for Pattersons

PATTERSON

ORIGIN-REMOVE

MIN-EMAP-PATTERSON

MAP-FILE

SUM-EMAP-PATTERSON

MIN-PATTERSONS

SUM-PATTERSONS

AUTO-PATTERSON

HARKER-ANALYSIS

NON-HARKER-ANALYSIS

NR-HEAVY-ATOMS


PATTERSON     cc

Calculate a Patterson function using E*E (if cc=EE), E*F (if cc=EF) or F*F (if cc=FF) as coefficients.

The default is cc=E*F.


ORIGIN-REMOVE

Remove the origin peak of a Patterson function. Note that this keyword will not work if the Patterson coefficients are E*F.


MIN-EMAP-PATTERSON     x1 y1 z1 x2 y2 z2 .....

Calculate a minimum function from an E-map and Patterson-map based on a few 'atoms' on the E-map.  Where  xn, yn and zn are the positinal parameters (fractional coordinates) of the nth 'atom'  used for the superposition. 'MIN-EMAP-PATTERSON' can be used effectively to remove spurious peaks on an E-map. For this purpose the program should be run twice: Firstly, run SAPI in a usual way to obtain an E-map, which should be saved for later use. Secondly, the program should be run with the keywords 'MIN-EMAP-PATTERSON' and MAP-FILE, the later is used to specify the path and file name of the E-map previously saved.


MAP-FILE

This keyword specifies the path and filename of an E-map or Fourier map, which was obtained from a previous run of SAPI and is to be used for a Patterson superposition with the keyword MIN-EMAP-PATTERSON or SUM-EMAP-PATTERSON.

Example:

MAP-FILE      e:\sapi\samples\zcw\zcwdp1.map


SUM-EMAP-PATTERSON     x1 y1 z1 x2 y2 z2 .....

Calculate a  sum function from an E-map and a Patterson-map. For further details see MIN-EMAP-PATTERSON.


MIN-PATTERSONS     x1 y1 z1 x2 y2 z2 .....

Calculate a Patterson-minimum function. Superposition will be done on the Harker peaks corresponding to the atomic site x1 y1 z1. if more than one independent atom is specified, the non-Harker peaks between atoms 1 and 2, atoms 1 and 3 ... will also be treated. MIN-PATTERSONS is particularly useful for extending a partial structure to the complete one, espectially when the partial structure can not dominate the phases to give a good Fourier map.


SUM-PATTERSONS     x1 y1 z1 x2 y2 z2 .....

Calculate a Patterson-sum function. For further details see MIN-PATTERSONS.


AUTO-PATTERSON

Automatic  Patterson  analysis. The program calculates first a Patterson map with E*F as coefficients. It then goes on to a Harker analysis to locate heavy atoms. Finally  a minimum function based on the heavy atom sites is used to find out the light atoms. All the controlling  parameters will be assigned by the program automatically according to the cell contents.


HARKER-ANALYSIS     n

Request the calculation of Patterson function followed by Harker-peak analysis based on the n largest Patterson peaks. The default value of n equals 10.


NON-HARKER-ANALYSIS     n

Request the calculation of Patterson function followed by non-Harker-peak analysis based on the n largest Patterson peaks. The default value of n equals 20.


NR-HEAVY-ATOMS     n

This keyword is to use with the keywords HARKER-ANALYSIS and NON-HARKER-ANALYSIS. The  program  will take the largest n 'atoms' from the output of Harker-peak analysis, assuming that they are all 'heavy-atoms' and then start a non-Harker-peak analysis. The default value of n is 1.

NR-HEAVY-ATOMS     x1 y1 z1   x2 y2 z2 .....xn yn zn

This keyword is to use with the keyword NON-HARKER-ANALYSIS in the absence HARKER-ANALYSIS. The program will read the atomic positions x1 y1 z1 ..... xn yn zn assuming they are all 'heavy-atoms' and then start a non-Harker-peak analysis. The maximum acceptable number of n is 40.


Keywords for direct methods
8.7   Keywords for direct methods

FIRST-PART-PHASE

LAST-PART-PHASE

SKIP-PHASE

NO-REJECTING-WWW

NO-MODIFICATION-PHASE

TANGENT-CONVENTIONAL

TANGENT-STATISTICAL-W

NR-E-FOR-PHASE

E-MAX

E-MIN

NR-PSIZERO

E-PSIZERO-MAX

KAPPA-MAX

KAPPA-MIN

NR-PHASES-TO-SOLVE

PR-FULL-CONVERGENCE

PR-PARTIAL-CONVERGENCE

SIGMA-1

NR-SPECIAL-HKL

NR-GENERAL-HKL

NR-SETS-TO-DEVELOP

SETS-TO-DEVELOP

NR-SKIP-SETS

NR-RANDOM-PHASES

WEIGHT-INITIAL

CODES-ORIGIN-FIXING

NO-ORIGIN-FIXING

CODE-ENANTIOMORPH

PHASES-KNOWN

WEIGHT-ABSFOM

WEIGHT-PSIZERO

WEIGHT-RESIDUAL

EARLY-FOM

CUT-A-EARLY-FOM

CUT-B-EARLY-FOM

PHASES-STARTING

SET-CHOSEN


FIRST-PART-PHASE

LAST-PART-PHASE

SKIP-PHASE

These keywords specify the path the direct-method program "PHASE. 'FIRST-PART-PHASE' runs the first part of "PHASE", which sets up the phase relationships and determines the origin and enantiomorph fixing reflections through a convergence procedure; 'LAST-PART-PHASE'  runs  the  second  part of "PHASE". 'SKIP-PHASE' halts the program immediately, i.e. no calculation takes place. If  none  of these is specified, both parts of the  program  are  run.  If  there is no any keyword  (including FAST-JOB) specified for "PHASE", the program will run as follows:

1. The program will generate a minimum number of phase sets equal to 10 or the number of independent atoms, whichever is the larger.

2. After finished phase development for these sets, if none of which has a psizero figure of merit less than 1.6 and a residual figure of merit less than 25, the program will continue to  generate new phase sets up to a total number of 100 or three times the minimum number of phase sets determined according to 1, whichever is the smaller.

3. The conventional weighted tangent refinement will be used at first. After finished phase development for the first 10 sets, if any one of the following conditions is fulfilled, the tangent refinement will change automatically to the statistical weighting mode and the phase development process will be restarted.

a) The averaged absolute figure of merit greater than 1.1 and the averaged deviation among the absolute figures of merit less than 0.1;

b) The averaged absolute figure of merit greater than 1.25;

c) The averaged deviation among the absolute figures of merit less than 0.02.


NO-REJECTING-WWW

This keyword informs the program not to reject the phase relationships involving three systematically  'weak' reflections in dealing with structures having pseudo-translational symmetry.

NO-MODIFICATION-PHASE

This keyword informs the program not to modify  the phase development process in dealing with structures having pseudo-translational symmetry.

In the absence of keywords NO-REJECTING-WWW and NO-MODIFICATION-PHASE,  "PHASE" will automatically handle a structure having pseudo-translational symmetry as follows:

All triplets composed of three 'weak' reflections will be eliminated in the sigma-2 list and the phase derivation will be devided into two stages. During the first stage only phases of the 'strong' reflections are developed, while in the second stage the phases of 'weak' reflections are derived by the phase relationships of the type 'weak-strong-weak'.


TANGENT-CONVENTIONAL

Requests the conventional weighted tangent formula. By default the program will always use conventional weighting scheme for the first 10 trials of phase development. This keyword is used only if the user wish to prevent the program from changing the weighting scheme to TANGENT-STATISTICAL-W after the first 10 trials.


TANGENT-STATISTICAL-W

Requests the statistically weighted tangent formula from the beginning through the end of phase development. This weighting scheme is useful in cases of pseudosymmetry and when the conventional weighting tangent formula gives over-consistent phases (typified by high absolute figures of merit).


NR-E-FOR-PHASE     n

Number of reflections with largest E-values to be passed on to the program "PHASE", subject to a minimum value of E(obs) = 1.2. The default is 4* number of independent atoms + 50  (if centro-symmetric) + 50 (if triclinic) + 150 to a maximum of 1000.


E-MAXIMUM x
E-MAX     x

The maximum value of largest E's to be passed on to the program "PHASE". The default is E(maximum) = 5.0.

E-MIN     x

The minimum value of largest E's to be passed on to the program "PHASE". If the total number of reflections is greater than 500 the default is E(minimum) = 1.2, otherwise it will be 0.9 .


NR-PSIZERO     n

Number of smallest E-valuse to be passed on to the program "PHASE" for use in the psizero figure of merit. If the total number of reflections is greater than 300 the default is 100, otherwise it will be 50.


E-PSIZERO-MAX     x

The maximum E-value for the calculation of psizero figure of merit. The default is 0.3.


KAPPA-MIN x
KAPPA-MAX     x

The program will not accept phase relationships with a kappa-value greater than x for use in phase determination. the default is 50.

KAPPA-MIN     x

The program will not accept phase relationships with a kappa-value less than x for use in phase determination. The default is 0.6 .


NR-PHASES-TO-SOLVE     n

The program will attempt to determine phases of the n reflections lowest in the convergence map. This has the effect of maximising the relationship to reflection ratio. The default is usually 50 less than the number of reflections passed by the program "PREPARE".


PR-FULL-CONVERGENCE

Produces a full listing of the convergence map.


PR-PARTIAL-CONVERGENCE

Produces a listing for 60 reflections at the bottom of convergence map. If both PR-FULL-CONVERGENCE and PR-PARTIAL-CONVERGENCE are not specified, the default is that no part of the convergence map is.


PROBABILITY x
SIGMA-1     x

The lower limit of probability for accepting a phase determined by the sigma-1 formula as one of the starting phases, subject to its having more than three contributing indications. The default value of x prevents any such phases entering the starting set.


NR-SPECIAL-HKL     n

The number of special reflections required to be at the bottom of convergence map. Special reflections are those whose phases are restricted to two values such as zero or 180 degrees. Note that in centro-symmetric space groups, all reflexions are special.


NR-GENERAL-HKLS n
NR-GENERAL-HKL     n

The number of  general  reflections required to be at the bottom of convergence  map. General reflections are those whose phases may take on any value.


NR-SETS-TO-DEVELOP     n

Maximum number of starting phase sets to be generated.


SETS-TO-DEVELOP     n

Where n is the number of phase sets specifically requested by the user. This keyword is followed by records with the serial numbers of the sets in ascending order in 20I4 format. There must be no more than 500 phase sets specified. This facility allows the generation of particular sets of phases from a previous run of the program.


NR-SKIP-SETS     n

The program will skip the first n random phase sets and start the phase development from the n+1 set onward.


NR-RANDOM-PHASES     n

This specifies the number, n, of reflections in the starting set. The default is 250 for normal structures and is 50 less than the numder of reflections passed to the program "PHASE" for those structures with pseudo-translational symmetry. In the latter case if the keyword NR-PHASES-TO-SOLVE     m is specified, n will not allowed to be greater than m-2.


WEIGHT-INITIAL     x

The weight for the initial random phases. The default is 0.25.


CODES-ORIGIN-FIXING  n n ..
CODES-ORIGIN-FIXING     n1 n2 ...

The codes of the required origin-fixing reflexions. Note that the program will choose the phase values for these reflections. The rules it follows are:

Special reflections: the value that lies between 0 and 179.

General reflections: 45 and 315 degrees.

If a general reflection also fixes the enantiomorph, it is given the single value of 45 degrees. If the user is dissatisfied with the origin chosen automatically by the program "PHASE", he may input one, two or three reflections of his own choice, and "PHASE" will choose the remaining reflections needed to define the origin.


NO-ORIGIN-FIXING

Origin fixing reflections should neither be chosen nor be checked by the program.


CODE-ENANTIOMORPH     n

The code of the required enantiomorph-fixing reflexion.


PHASES-KNOWN     n1 n2 n3 ...

This specifies the code, phase, weight (all integers) of each known phase. n2 should be in degrees. n3 can be a value from 1 to 100. A weight greater than 99 will be interpreted as meaning certainty, and the phase will be fixed during tangent formula refinement. Note that the phase value must relate to the origin chosen by the program "PHASE". The maximum number of known phases allowed is 250.


WEIGHT-ABSFOM     x

The weight of the absolute figure of merit used for calculating the combined figure of merit. The default is 0.2

WEIGHT-PSIZERO     x

The weight of the psi-zero figure of merit used for calculating the combined figure of merit. The default is 1.4

WEIGHT-RESIDUAL     x

The weight of the R(alpha) figure of merit used for calculating the combined figure of merit. The default is 1.4


EARLY-FOM

Specifies that the early figures of merit are to be applied.


CUT-A-EARLY-FOM     x

The initial cutoff of the first early figure of merit. This figure of merit is calculated as a psizero figure of merit with a weighted residual, and sets with a figure of merit greater than the cutoff are rejected. As sets are accepted, the cutoff gradually reduces. the default x is 1.8. If 'CUT-A-EARLY-FOM' is given, EARLY-FOM is automatically assumed. If 'CUT-A-EARLY-FOM     0' is given, the first early figure of merit is not used.


CUT-B-EARLY-FOM     x

The cutoff for the second early figure of merit. This is a simple psizero test, and sets with a figure of merit greater than the cutoff are rejected. The default x is 1.6. if 'CUT-B-EARLY-FOM' is given, EARLY-FOM is automatically assumed.


PHASES-STARTING     n

The number of starting phases input to the tangent formula to a maximum of 3/2 (250). The parameter is followed by formatted data:

Codes of the starting phases (20I4)

Markers of the starting phases (20I4)

=  1 if the phase can vary from the start.

= -1 if the phase is kept fixed until the last cycle.

Weights (0.0 to 1.0) of the starting phases in (20F4.2).

All origin and enantiomorph defining phases must have a weight of 1.0

Then follow sets of records with the phases, in degrees, of the n starting phases in (20I4) format with a set identification number in field n+1. Data are terminated with a dummy set of phases with the set identification number equal to zero.


SET-CHOSEN     n

Generate an E-map using the phases from set number n. The default is that, phases from the set having the highest combined figure of merit should be used.


Keywords for map calculation and interpretation
8.8   Keywords for map calculation and interpretation

GRID-SPACING-FFT

NR-PEAKS-TO-LIST

ATOMS-ADDITIONAL

NO-JOIN

DISTANCE-MAX

BOND-MIN

BOND-MAX

ANGLE-MIN

ANGLE-MAX

NR-IONIC-ATOMS


GRID-SPACING-FFT     x

The grid on which the map is evaluated will have a spacing of approximately x angstroms. The default is 0.28 angstroms. This value will increased automatically to keep the size of some arrays of the program not exceeding certain limit.


NR-PEAKS-LIST n
NR-PEAKS-TO-LIST     n

n is the number of peaks to be searched for in the map. The default is (11*nb)/9 where nb is the number of independent atoms (excluding hydrogens). If two clusters are within 2.8 angstrom of each the default is automatically increased to (3*nb)/2. In any case, at least 30 peaks will be printed out.


ATOMS-ADDITIONAL     n

n is the number of additional atoms input by the user to be included in the interpretation of the map. (number of peaks + number of additional atoms must be less than 200). If 'ATOMS-ADDITIONAL' is specified, the record followed has the run time format for reading the n sets of atomic coordinates (e.g. (3F10.5) ). Then follow n records with the atomic coordinates in that format. This facility will normally be used when a difference Fourier is being interpreted. The inclusion of the subtracted atoms ensures that they are included in the bond lengths and angles calculations, and also that they appear in the lineprinter picture of the structure.


NO-JOIN

Requests not to interprete the peaks for connectivity. The program prints a list of the highest peaks and then stops. This condition is set automatically if no chemical bonds can be found by the program.


DISTANCE-MAX     x

Interpeak distances less than x are tabulated. The default is 2.4 angstroms.


BOND-MIN     x

Minimum allowed bond length in the interpretation. The default is 1.1 angstroms.

BOND-MAX     x

Maximum allowed bond length in the interpretation. The default is 1.95 angstroms.


ANGLE-MIN     x

Minimum allowed bond angle in the interpretation. The default is 85 degrees.

ANGLE-MAX     x

Maximum allowed bond angle in the interpretation. The default is 145 degrees.


NR-IONIC-ATOMS     n

The number of ionic atoms in the asymmetric unit. When performing an interpretation of a cluster, the program will assume that the n highest peaks correspond to these ionic atoms. They will not be included in the interpretation, and all peaks within the maximum bond length will be marked as spurious. This is useful when the compound contains an atom ionically bonded to the organic part of the molecule. Using this facility will prevent spurious peaks caused by diffraction ripples around the ion being interpreted as atoms.


Index for keywords
10.   Index for keywords

A

ANGLE-MAX

ANGLE-MIN

Atomic parameter specification

ATOMS-ADDITIONAL

AUTO-PATTERSON

B

B-FACTOR

BOND-MAX

BOND-MIN

C

CELL-CLUSTER

CELL-DIMENSIONS

CLUSTER-ORIENTED

CLUSTER-POSITIONED

CLUSTER-RANDOM

CODE-ENANTIOMORPH

CODES-ORIGIN-FIXING

CONTENTS-UNIT-CELL

CUT-A-EARLY-FOM

CUT-B-EARLY-FOM

D

DATA-FILE-HKL

DISTANCE-MAX

E

E-HKL-INPUT

E-MAX

E-MIN

E-PSIZERO-MAX

E-SQUARE-MAX

EARLY-FOM

END

F

FACTORS-ATOMIC

FAST-JOB

FIRST-PART-PHASE

FOURIER-DIFFERENCE

FOURIER-WEIGHTED

G

GRID-SPACING-FFT

GROUP-HKL

H

HARKER-ANALYSIS

K

K-CURVE

KAPPA-MAX

KAPPA-MIN

KARLE-RECYCLING

L

LAST-PART-PHASE

LIMIT-RESOLUTION

M

MAP-FILE

MIN-EMAP-PATTERSON

MIN-PATTERSONS

MISSING-HKL

N

NO-AUTOGP

NO-JOIN

NO-MODIFICATION-PHASE

NO-ORIGIN-FIXING

NO-REJECTING-WWW

NON-HARKER-ANALYSIS

NR-CLUSTER-RANDOM

NR-E-FOR-PHASE

NR-GENERAL-HKL

NR-GROUPS-SPECIFIED

NR-HEAVY-ATOMS

NR-IONIC-ATOMS

NR-PEAKS-TO-LIST

NR-PHASES-TO-SOLVE

NR-POINTS-WILSON

NR-PSIZERO

NR-RANDOM-PHASES

NR-SETS-TO-DEVELOP

NR-SKIP-SETS

NR-SPECIAL-HKL

O

ORIGIN-REMOVE

P

PATTERSON

PHASES-KNOWN

PHASES-STARTING

PR-FOBS-E

PR-FULL-CONVERGENCE

PR-PARTIAL-CONVERGENCE

R

RATIO-ST-TL

REMARKS

RESCALE-PARITY-GROUP

RHO-MAX

S

SCALE-GROUP

SET-CHOSEN

SETS-TO-DEVELOP

SIGMA-1

SKIP-PHASE

SKIP-PREPARE

SOLVE-ENANTIOMORPH

SPACE-GROUP

SUM-EMAP-PATTERSON

SUM-PATTERSONS

T

TANGENT-CONVENTIONAL

TANGENT-STATISTICAL-W

W

WEIGHT-ABSFOM

WEIGHT-INITIAL

WEIGHT-PSIZERO

WEIGHT-RESIDUAL

WEIGHT-UNITY

WILSON-GROUP


I/O Channels and temporary files

All  programs  in  the  system  use  channel  5 to input keyword information. The program "PREPAR" will accept a free format  input  file and  then  change  it  into  a formated one, which will be read later by other programs through the same channel.

All programs in the system use channel 6 for printer output.

All  the  files  listed  below  have a run-time prefix, which is automatically  determined  according  to  the names of the data file and keyword file used. For example if you are running a job with a data file named  CORT.XXX  and  a  keyword  file  named  ZZZ.KEY1  then  the  file '_PHASDT.TM' below will actually has the name 'CORTKEY1_PHASDT.TM' while the file '_.PKS1' will be 'CORTKEY1_.PKS1'. On the other hand, when SAPI is called via TEXSAN, the prefix will always be 'SAPI'.

Channels and files for "PREPAR"

Channels and files for "PHASE"

Channels and files for "EXFFT"

Channels and files for "SEARCH"


Channels and files for "PREPAR"

Channel	File name	Format	Contents
1	_PHASDT.TM	Formatted	h, k, l, E ...     values output from"PREPAR" to be read by "PHASE".
2	_FCOEF.TM	Unformatted	Fourier coefficients output from"PREPAR" for calculating an F-map or P-map using "EXFFT".
3	_DAT.TM	Formatted	A copy of the data file which is used as input of "PREPAR".
4	_KARLE.TM	Formatted	Output from "PREPAR" for Karle recycling by "PHASE".
5	_KEY.TM	Formatted	A copy of the keyword file used as input of "PREPAR".
5	_PHASKW.TM	Formatted	Output controlling parameters for running "PHASE".
6	_OUT1.TM	Formatted	Line printer output results from "PREPAR".
7	_SCRA7.TM	Unformatted	Scratch file
8	_SCRA8.TM	Unformatted	Scratch file
10	_EXFFKW.TM	Formatted	Output controlling parameters for running "EXFFT".
11	_SEARKW.TM	Formatted	Output controlling parameters for running "SEARCH"
15	_.PKS1	Formatted	Peak list to be read by "PREPAR" for running automatic Patterson analysis and for calculating Patterson-minimum functions 'PPM' and 'PEM'.


Channels and files for "PHASE"

Channel	File name	Format	Contents
1	_PHASDT.TM	Formatted	Input data to "PHASE" created by "PREPAR" for ab-initio direct-method phasing.
2	_FCOEF.TM	Unformatted	Output E-values and phases for calculating an E-map by "EXFFT".
3	_SIGMA2.TM	Unformatted	SIGMA2 relationships.
4	_KARLE.TM	Formatted	Input data of "PHASE" created by "PREPAR" for Karle recycling.
5	_PHASKW.TM	Formatted	Controlling file of "PHASE" created by "PREPAR".
6	_OUT2.TM	Formatted	Line-printer output results from "PHASE".


Channels and files for "EXFFT"

Channel	File name	Format	Contents
1	_MAP.TM	Unformatted	A resulted map from "EXFFT".
2	_FCOEF.TM	Unformatted	Input Fourier coefficients created by "PREPAR" or "PHASE".
3	_SCRA3.TM	Unformatted	Scratch file, access=direct.
4	_SCRA4.TM	Unformatted	Scratch file, access=direct.
	or
	_.EMAP	Unformatted	A previously calculated E-map to be read by "EXFFT".
5	_EXFFKW.TM	Formatted	Controlling file of "EXFFT" created by "PREPAR".
6	_OUT3.TM	Formatted	Line-printer-output results from "EXFFT".
7	_SCRA7.TM	Unformatted	Scratch file, access=direct.
8	_SCRA8.TM	Unformatted	Scratch file.
	or
	_.PKS2	Formatted	Peak list output from "EXFFT" to be read by "SEARCH".


Channels and files for "SEARCH"

Channel	File name	Format	Contents
1	_MAP.TM	Unformatted	A map from "EXFFT" to be read by "SEARCH".
5	_SEARCH.TM	Formatted	Control file of "SEARCH" created by "PREPAR".
6	_OUT4.TM	Formatted	Line-printer-output results from "SEARCH".
7	_.PKS1	Formatted	Peak list output from "SEARCH".
8	_.PKS2	Formatted	Peak list output from "EXFFT" to be read by "TEXSAN".


Toolbar
The Toolbar

The Toolbar is a row of buttons at the top of the main window which represent application commands. Clicking one of the buttons is a quick alternative to choosing a command from the menu.  Buttons on the toolbar activate and deactivate according to the state of the application.

Button	Action	Menu Equivalent

Create a new document	File|New

Locate and open a file	File|Open

Save the file in the active window	File|Save

Cut selected text to Clipboard	Edit|Cut

Copy selected text to Clipboard	Edit|Copy

Paste text from Clipboard	Edit|Paste

Undo previous editor action	Edit|Undo

Search for text	Search|Find

Repeat last Find or Replace operation	Search|Next

Print the active window	File|Print

Display help file contents	(None)


Windows Keys

Cursor Movement Keys

Dialog Box Keys

Editing Keys

Help Keys

Menu Keys

System Keys

Text Selection Keys

Window Keys


Cursor Movement Keys

Key(s)	Function

Arrow key	Moves the cursor left, right, up, or down in a field.

End or Ctrl+Right Arrow	Moves to the end of a field.

Home or Ctrl+Left Arrow	Moves to the beginning of a field.

Pape Up or Page Down	Moves up or down in a field, one screen at a time.


Dialog Box Keys

Key(s)	Function

Tab	Moves from field to field (left to right and top to bottom).

Shift+Tab	Moves from field to field in reverse order.

Alt+letter	Moves to the option or group whose underlined letter matches the one you type.

Arrow key	Moves from option to option within a group of options.

Enter	Executes a command button.

Or, chooses the selected item in a list box and executes the command.

Esc	Closes a dialog box without completing the command. (Same as Cancel)

Alt+Down Arrow	Opens a drop-down list box.

Alt+Up or Down Arrow	Selects item in a drop-down list box.

Spacebar	Cancels a selection in a list box.

Selects or clears a check box.

Ctrl+Slash	Selects all the items in a list box.

Ctrl+Backslash	Cancels all selections except the current selection.

Shift+ Arrow key	Extends selection in a text box.

Shift+ Home	Extends selection to first character in a text box.

Shift+ End	Extends selection to last character in a text box


Editing Keys

Key(s)	Function

Backspace	Deletes the character to the left of the cursor.

Or, deletes selected text.

Delete	Deletes the character to the right of the cursor.

Or, deletes selected text.


Help Keys

Key(s)	Function

F1	Gets Help and displays the Help Index for the application. If the Help window is already open, pressing F1 displays the "Using Windows Help" topics.

In some Windows applications, pressing F1 displays a Help topic on the selected command, dialog box option, or system message.

Shift+F1	Changes the pointer to [image] so you can get Help on a specific command, screen region, or key. You can then choose a command, click the screen region, or press a key or key combination you want to know more about.

(This feature is not available in all Windows applications.)


Menu Keys

Key(s)	Function

Alt	Selects the first menu on the menu bar.

Letter key	Chooses the menu, or menu item, whose underlined letter matches the one you type, when a menu has focus.

Alt+Letter key	Pulls down the menu whose underlined letter matches the one you type.

Left or Right Arrow	Moves among menus of the main menu bar.

Up or Down Arrow	Moves among menu items within a drop-down menu.

Enter	Chooses the selected menu item.


System Keys

The following keys can be used from any window, regardless of the application you are using.

Key(s)	Function

Ctrl+Esc	Switches to the Task List.

Alt+Esc	Switches to the next application window or minimized icon, including full-screen programs.

Alt+Tab	Switches to the next application window, restoring applications that are running as icons.

Alt+PrtSc	Copies the entire screen to Clipboard.

Ctrl+F4	Closes the active window.

F1	Gets Help and displays the Help Index for the application. (See Help Keys)


Text Selection Keys

Key(s)	Function

Shift+Left or Right Arrow	Selects text one character at a time to the left or right.

Shift+Down or Up	Selects one line of text up or down.

Shift+End	Selects text to the end of the line.

Shift+Home	Selects text to the beginning of the line.

Shift+Page Down	Selects text down one window.

Or, cancels the selection if the next window is already selected.

Shift+Page Up	Selects text up one window.

Or, cancels the selection if the previous window is already selected.

Ctrl+Shift+Left or Right Arrow	Selects text to the next or previous word.

Ctrl+Shift+Up or Down Arrow	Selects text to the beginning (Up Arrow) or end (Down Arrow) of the paragraph.

Ctrl+Shift+End	Selects text to the end of the document.

Ctrl+Shift+Home	Selects text to the beginning of the document.


Window Keys

Key(s)	Function

Alt+Spacebar	Opens the Control menu for an application window.

Alt+Hyphen	Opens the Control menu for a document window.

Alt+F4	Closes a window.

Alt+Esc	Switches to the next application window or minimized icon, including full-screen programs.

Alt+Tab	Switches to the next application window, restoring applications that are running as icons.

Alt+Enter	Switches a non-Windows application between running in a window and running full screen.

Arrow key	Moves a window when you have chosen Move from the Control menu.

Or, changes the size of a window when you have chosen Size from the Control menu.


Set option: Direct methods


Set option: Pattersons


Set option: Fourier Synthesis


Direct methods / Normalization


Direct methods / Phase derivation


Direct methods / E-map calculation


Patterson / Analysis of Patterson Peaks


Patterson / Self-superposition


Patterson / Superposition with others


Temperature and scaling factors


Direct methods / Use patial structure


Atomic scattering factors


Index relations specified for reflection groups


Phase derivation / Es input


Phase derivation / Phasing control


Phase derivation / Partial structure


Direct methods / Partial structure / Random cluster


Correct Keyword Dialog


Find Dialog


Replace Dialog


Interpretation of the resultant map


New Keyword File Dialog


XYZ Dialog


XYZF Dialog