Quick Start Users Guide for
Bruker SMART APEX II Diffractometer
APENDIX III
INTRODUCTION FOR FINDING ADDITIONAL SYMMETRY
WITH PLATON
J. Tanski 2/12/06
Platon is a versatile SHELX97 compatible multipurpose crystallographic tool and is
FREE for academic users. More information can be found from Platon homepage.
Suppose your files are f10.*
(1)
In DOS mode, type copy f10.res f20.res, and then type copy f10.hkl f20.hkl. In
this introduction, f20.* will be used while f10.* will be kept for backup.
(2)
Find the Platon program on the computer, double click pwt.exe to open Platon
Taskbar and the following window will show up.
(3)
In Platon, click File and select select Data File. Either .ins or .res file can be used.
However, .res file is recommended. Click Files of type and select SHELX file
(*.res), then find the target file f20.res by browsing the computer through the
Look in window, then click open to select f20.res file.
(4)
Find the icon
∑
∫
fx
on the toolbars and click it. A lot of numbers will come out on
the screen at this time and it usually takes a few seconds but up to a couple of
minutes. It’s done when you see the bottom of the screen have something like
following:
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Summary and Remarks : N = NOTE, W = WARNING, E = ERROR
You may see the summary of results from Platon on the screen.
(5)
Close Platon program and any other windows that were opened by Platon.
(6)
Use Windows Explorer to go to the directory of your files and double click f20.lps
to open it. Go to the end of this file and find lines of (Summary and Remarks : N
= NOTE, W = WARNING, E = ERROR). Pay attention to those warning
messages. If additional symmetry was found, you will see a message like this: N:
ADDSYM finds additional \(pseudo\)symmetry in the structure \(please
check!\). Check that there are no solvent accessible voids; if there are, there may be
disordered solvent that can be modeled or treated with SQUEEZE. PLATON also
tells your about possible hydrogen bonds; if there are, insert HTAB in the .ins and
run XL again. Close f20.lps.
(7)
If no additional symmetry was found, finish the structure as usual using files f10.*.
Otherwise, the structure needs to be converted to the proper space group. In Platon
Taskbar, select the data file again click Start and select Graphical Menu. A
graphical menu will show up.
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(8)
Under the column of SYMMETRY, click ADDSYM-SHX and wait for a few
seconds until it’s done. Platon will make changes to f20.res file. Then click Exit
on the right bottom corner to exit graphical menu. Close Platon program and any
other windows that were opened by Platon.
(9) Open
f20.res with Notepad. The title has been changed to this:
TITL XXXXXX in P-1 P21/c
The first P-1 is the previous space group and P21/c is the new space group. Change
the title properly by deleting previous space group P-1.
Sometimes, Platon uses non-standard settings. For example in this case, P2(1)/c
should be used instead of P2(1)/n. Make sure that the new space group is correct
by referring to the new symmetry operations.
(10) SFAC and UNIT lines have been changed to:
SFAC C 2.31000 20.84392 1.02000 10.20751 1.58860 0.56870 0.86500 =
51.65125 0.21560 0.00330 0.00160 11.500 0.68000 12.01000
SFAC H 0.49300 10.51091 0.32291 26.12573 0.14019 3.14236 0.04081 =
57.79977 0.00304 0.00000 0.00000 0.624 0.35000 1.00800
UNIT 92 60
Manually create SFAC lines to be SFAC C H, and make sure the order of atom is
the same as in atom list. Put this line just before UNIT instruction as usual.
Delete current SFAC lines with a lot of numbers. New SFAC and UNIT lines
should look like this:
SFAC C H
UNIT 92 60
IMPORTANT !
Several things have been changed from the initial .res file to that output by
Platon. Make sure all commands present in the saved f10.res are copied
appropriately into the new f20.res.
Platon may also change the atom codes in the atom list, make sure to fix these!
Save f20.res after change and then quit.
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(11) In DOS mode, type copy f20.res f20.ins to create f20.ins file.
(12) In DOS mode, type copy f10.pcf f20.pcf to create f20.pcf file. .pcf file contains
crystal information needed as a reference when XCIF runs. Open f20.pcf with
Notepad, check _symmetry_cell_setting and
_symmetry_space_group_name_H-M at the beginning of the file.
In this case, change _symmetry_cell_setting from Triclinic to Monoclinic;
Change _symmetry_space_group_name_H-M from P-1 to P2(1)/c. Save
f20.pcf and quit.
(13)
In DOS mode, run XL f20. Now the structure is in the new symmetry. Finish as
usual. During XCIF, make sure the correct space group name is printed.
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