shelxtl用户指南
[color=red][quote]（哇，这样看着好累，兄弟不能做成word或pdf分享吗？可以把附件放到免费空间，见置顶“指南贴”）by 大风[/quote][/color]
A Guide to Using SHELXTL
Gregory S. Girolami, Julia L. Brumaghim, James G. Priepot, and Jon P. Goveia
24 January 2000
SHELXTL NT Version
1. SHELXTL programs and files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2. General Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3. Preparing for X-ray work-up. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
4. Setting up for the refinement – XPREP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
5. Solving by direct methods – XS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
6. Assessing the solution – XP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
7. Solving by Patterson methods – XS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
8. What to do when you can’t find a solution . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
9. Editing the .ins file generated by XP. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
10. Least squares refinement – XL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
11. Checking for missed crystallographic symmetry – PLATON . . . . . . . . . . . . . . 21
12. Turning atoms anisotropic and adding hydrogen atoms . . . . . . . . . . . . . . . . . . 22
13. Correcting for absorption – XPREP. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
14. Extinction, weighting schemes, and absolute configuration. . . . . . . . . . . . . . . . 28
15. Final details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
16. Generating graphical displays – XP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
17. Printing diagrams generated by XP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
18. Miscellaneous XP commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Appendix 1. Sample structure report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 1. SHELXTL programs and files
1.1) SHELXTL programs
SHELXTL is a software package that is useful for solving and refining single-crystal Xray
diffraction data sets. SHELXTL consists of four major programs, which are:
XPREP – Space group determination, absorption corrections, unit cell
transformations, and reciprocal space plots. XPREP reads the raw data file
filename.raw and the parameter file filename.p4p written by the diffractometer
control program, and writes the instruction file filename.ins and reflection data
file filename.hkl for use by the programs XS and XL.
XS – Structure solution by direct methods or Patterson methods. XS reads
filename.hkl and filename.ins (generated by XPREP) and writes the best solution
(a list of atomic coordinates plus other information) to the results file
filename.res. A detailed listing of the program’s activities are written to the file
filename.lst.
XL – Least-squares structure refinement. XL reads filename.ins (obtained by
renaming the filename.res file generated by XS or by a previous XL refinement
cycle) and writes a new results file filename.res and listing file filename.lst.
XP – Interactive molecular graphics and publication-quality diagrams. XP reads the
filename.res from XS or XL and (if so desired) can (re)write the filename.ins file
for the next series of refinements.
1.2) SHELXTL files
SHELXTL uses files of the type ‘filename.ext’, where filename is a name of up to eight
alphanumeric characters, and ext is a three character extension. Unless you change them,
files for a given problem will always have the same filename but different extensions. The
extensions define the function of each file and are generated or recognized automatically
by the SHELXTL programs. The file extensions used by SHELXTL are:
.raw – raw reflection data; used as input file for XPREP
._ls – statistical analysis of raw reflection data
.prp – a listing of what was done while running XPREP
.p4p – data collection parameter file; used as input file for XPREP
.hkl – reflection intensity table created by XPREP.
.ins – instruction file containing cell parameters, etc. created by XPREP;
input file for XS, XL, and XP
.res – results file created by running XS or XL; updated form of .ins file
.lst – a listing of what was done in the last computer run.
1.3) Solving a crystal structure
The flowchart on the following page briefly outlines the steps necessary to solve an X-ray
crystal structure by the methods discussed in this handout. It includes everything from
X-ray data collection to printing out a plot of the newly characterized molecule.
This handout does not, however, discuss how to handle disorder, non-integral site
occupancy factors, or restraints. A separate handout is available that deals with these
issues. Consult an expert for help if you encounter these problems.
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Data Collection X-ray detector
original.raw, original.p4p, original._ls
XPREP original
filename.ins and filename.hkl
XS filename XS filename
XL filename
Final cycles of least squares
XP absfile.res
Space Group Determination
Direct Methods (TREF) Patterson
Heavy Atom Method (PATT)
Direct Methods
Fail
Patterson Methods
Fail
Least Squares Refinement
Further Refinements
- anisotropic refinement
- H atom refinements
Absorption Correction
Plot Generation
XPREP original
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2. General Procedures
2.1) Almost all commands that you type in must be followed by hitting the <enter> key. In
this handout, this is implicit; you will not be reminded that hitting the <enter> key is
necessary.
2.2) It is useful to make regular backup copies of key files (especially .ins files). To do
this, go to the Edit pull-down menu, and open the file of interest. Then go to the File pull
down menu, click on Save As, and type in a new name for the backed-up file (e.g.,
bkup1.ins). Note: the filename must be eight characters or shorter and must consist only
of letters and numbers.
NOTE: The SHELXTL software is unforgiving of mistakes in file handling – it is very
easy to corrupt the .ins file and undo all the work you have done. If you make backups
regularly, then you will be able to recover easily from data handling mishaps: simply
open the most recent backed-up file, use the Save As command to rename it filename.ins,
and continue with your refinement. If you do not make regular backups, then you risk
having to redo steps you have already done.
2.3) Some editing of text files will be necessary. The editor used in this laboratory is
Wordpad; below is a summary of some of the keyboard-activated commands used in this
text editor:
↑, ↓, ←, and → keys Moves cursor around the document
<delete> and <backspace> Deletes characters
<alt> f Opens File pull-down menu; commands listed below:
o Open file
s Save file
x Exit file
p Print file
<alt> e Opens Edit pull-down menu; commands listed below:
u Undo last action
a Select all text
t Cut selected text
c Copy selected text
p Paste selected text
l Delete selected text
To highlight a certain portion of text to edit, hold down the <shift> key and use the ↑, ↓,
←, and → keys to move the cursor. Alternatively, you may use a mouse.
3. Preparing for X-ray work-up
3.1) The diffraction data you will solve has already been transferred to your computer. All files
are stored in the Data folder on the desktop. To view a list of files in your folder, double
click on the Data icon.
3.2) Look in your Data folder and make sure that the original.raw and original.p4p files are
present, where original is a name that has been assigned to the files by the
crystallographer who collected the data (e.g., w25r). The .raw file is a list of the
reflection intensities sorted by Miller index. The .p4p file (and ._ls file, if present)
contain summaries of the data collection parameters and include the unit cell constants.
3.3) Next, you must tell the software which file contains your data. You do this by defining a
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“project”. First, open the SHELXTL window by double clicking the SHELXTL icon.
3.4) Start a new project by clicking Project, dragging to New, and then releasing. Navigate
through the folders (if necessary) until you see the original.raw file displayed in the
window. Type in a name for the project and write it down - we recommend using the
same name as the name of the .raw file. Then highlight the original.raw file with your
mouse, and click Ok.
3.5) You should now see a window that has your project name and path. To view this window
at any other time, click Project in the SHELXTL window, drag to Open, and release. 把全文拿出来分享吧？ 4. Setting up for the refinement – XPREP
4.1) Now you are ready to run XPREP, which is a program that will help you decide on a
space group and set up the files necessary to solve your structure. With the SHELXTL
window open, click on XPREP, drag to XPREP, and release.
4.2) XPREP will read the cell parameters (a b c α β γ) from the .p4p file. If no .p4p file is
present, XPREP will ask you to enter these parameters manually. To do this, simply enter
the appropriate values for a b c α β γ with spaces in between.
4.3) XPREP will next read and analyze the diffraction data in the .raw file. The first analysis
is a table of lattice conditions. The table is headed P (primitive), A, B, C (end-centered),
I (body-centered), F (face-centered), Obv, and Rev. Look at the last number in each
column, which gives the average value of the intensities for that lattice condition divided
by the error (I/σ). If, for any column, the value of I/σ is 3 or less (or significantly smaller
than the values in all the other columns), the condition is a likely one for your crystal (the
smaller the number, the better).
Usually, XPREP recommends which lattice condition is best; this recommendation is
enclosed in brackets, e.g. [P]. If this is the case, hit <enter> to accept XPREP’s choice
and go to step 4.4, unless you have reasons to do otherwise.
If XPREP has trouble recommending a lattice condition, it will show a question mark
enclosed in brackets [?]. If this happens, look to see which lattice condition has the
smallest number in the last line (smallest value for I/σ). Type in the letter corresponding
to your choice (P, A, B, C, etc.), unless you know from an earlier attempt to solve the
structure that this choice may not be correct. Then go to step 4.4
4.4) You should now be back in the XPREP main menu, and the suggested option should be to
look for higher symmetry [H]. Hit <enter> to accept this option.
XPREP will first print out some information that you can ignore, and then it will display
one or more options for the crystal system; each choice is printed in between -----------
dashed lines. (The seven possible crystal systems are triclinic, monoclinic, orthorhombic,
tetragonal, trigonal, hexagonal, and cubic). Record the possibilities with low FOM values
(FOM = figure of merit; note: triclinic always has FOM = 0). Ignore the comment
below the table about the original cell.
4.5) If XPREP makes a recommendation for a crystal system, the recommendation will be
enclosed in brackets, e.g. [A], which stands for choice A. Hit <enter> to accept its choice
unless you know it to be wrong, and then go to step 4.6.
If XPREP has difficulty choosing a crystal system for the unit cell (it will show [?]
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instead of a letter), it is best to pick the highest symmetry crystal system listed among the
possible choices (for example, pick orthorhombic over monoclinic, and monoclinic over
triclinic), unless you know that the higher symmetry choice does not lead to a solution of
the data. Type in the appropriate letter of the best option, hit <return>, and go to step 4.6.
4.6) After the search for higher symmetry is done, you will be back in the main menu and the
suggested option will be [S] to enter the space group determination routine. Hit <enter>.
4.7) The next suggested option will also be [S] to determine the space group. Hit <enter>.
XPREP will then suggest a crystal system (triclinic, etc.). Choose the same crystal
system as you did in step 4.4.
4.8) XPREP will then go through the lattice condition routine and make a suggestion
(primitive, etc.). Choose the same option as you did in step 4.3.
4.9) Next, XPREP will give a table of possible space groups. If at least one space group
appears in the table, go to step 4.10.
Occasionally, XPREP will be unable to find any space group that agrees with the
systematic absences it finds. In such cases, go back to the XPREP main menu by hitting
<enter> and change the tolerances (choice T). Make the minimum I/sigma gap (choice
G) half of its current size and the maximum mean I/sigma (choice A) twice its current
size. Choose the E option to exit to the XPREP main menu and then continue with step
4.4.
In some cases, XPREP will refuse to identify a space group even after adjusting the
tolerances, and you will have to decide yourself what the systematic absences are. Look
at the last two rows of the systematic absence exceptions table. A systematic absence is
likely if <I> or <I/σ> is significantly less than “normal”. From these decisions, you
should be able to guess a space group. Consult an expert if in doubt. Enter the space
group manually by typing its symbol (use a minus signs and parentheses to indicate
rotoinversion and screw axes, respectively: thus P-1 or P2(1)/c). Then go to step 4.10.
4.10) In the table of possible space groups, the last number in each row is the CFOM number
(which stands for combined figure of merit) for each space group. Usually, the smaller
the CFOM, the better. If CFOM is 2 or less, the space group choice is a good one
(although not necessarily the right one!). If it is 12 or greater, you will probably have
problems solving the data set in that space group.
Write down the three or four space groups that have the lowest values of CFOM (if there
are that many). Record the CFOM values for each.
Look at the space group with the lowest value of CFOM. If it is a centrosymmetric space
group, go to step 4.11.
If the space group with the lowest value of CFOM is chiral or non-centrosymmetric, then
answer the following two questions:
a) Is there a centrosymmetric space group whose CFOM is within 3 units of the
CFOM of the “best” space group?
b) Does your crystal contain heavy scatterers (for Mo radiation, atoms with Z
greater than 18)?
If the answer to either question is no, go to step 4.11.
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If the answer to both questions is yes, it is likely that the actual space group is the
centrosymmetric space group with the lowest CFOM. Skip step 4.11 and override
XPREP’s choice in step 4.12. If it proves impossible to find a solution in the
centrosymmetric space group, you can always re-run XPREP to choose a different one.
4.11) Above the table of systematic absence exceptions is a number, labeled Mean |E*E-1|,
which has been calculated from the data in the .raw file. Compare the value with those
expected for centrosymmetric and non-centrosymmetric space groups. If the Mean |E*E-
1| value is closer (say) to that expected for a centrosymmetric space group, then you
should check to make sure that the space group chosen by XPREP (or by you) is also
centrosymmetric. If it isn’t, it may be the wrong space group.
NOTE: Heavy scatterers (atoms with Z > 18) can distort the Mean |E*E-1| value and
make it an unreliable indicator of whether the cell is centrosymmetric or not.
4.12) XPREP will give a recommended space group in brackets: e.g. [F] for option F. If you
like XPREP’s recommended choice, accept it by hitting <enter> and go to step 4.13.
If you wish to choose a different space group than the one recommended by XPREP (or if
XPREP can’t decide and shows [?] as its choice), type the letter corresponding to the
option you think is best (see steps 4.10 and 4.11), then hit <enter>, and go to step 4.13.
4.13) After you have chosen a space group, a screen will come up with a table of information
about the current data set. Write down the space group, and from the line that reads
“current cell”, write down the values of a, b, c, α, β, γ, and the volume of the unit cell V,
which appear in that order.
4.14) Hit <enter>. XPREP will then display a chemical formula for the compound or ask you
to provide one. If the formula is not present, enter it manually (the program understands
abbreviations such as Me, Et, Ph, etc.). If the formula is incorrect, type F and enter the
correct formula.
4.15) Check the value that XPREP has calculated for Z (the number of formula units per unit
cell). For organic and many inorganic molecules, a rough calculation for Z can be done
manually:
Z ≈ (volume of unit cell in
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