Hello, I am sure that you have found that if you apply the symmetry operations
yourself, the resulting molecules can come out miles apart, so you need to find
the right unit cell translations that bring them close together again to
generate the real crystal packing. Coot does all this very well indeed (happy
new year, Paul). In the old ccp4i suite, there is CONTACT and NCONT which you
can find in the program list or even more if you are happy to use the command
line. I think I would have a look at the documentation, etc, for CONTACT.
On Friday, 10 January 2020, 20:41:27 GMT, orly avraham
<[email protected]> wrote:
Hi all,
I am a crystallographer currently employing computational methods as well as
experimental crystallography.I am trying to generate symmetry mates in python
(working with pandas dataframes), in order to analyze inter-sub-unit
interactions. To do so I am trying to use the info in "REMARK 290
CRYSTALLOGRAPHIC SYMMETRY" and manually (using numpy) perform a matrix
multiplication with the relevant translation (xyz*rotation + translation). For
some reason this doesn't work consistently and I feel I need to use the info in
CRYST1 to obtain the unit cell and multiplication matrix. Here I ran into
trouble with extracting the correct symmetry operations based on each space
group. I found spglib but it doesn't quite solve the problem.I also tried
opening PyMol through the command and generating symmetry mates this way. It
worked on a few files but failed quite quickly (segmentation fault) and was
also very slow.
Can anyone suggest a useful solution, preferably clear to use and/or well
documented? Or even have a python script/code they can share for this?
Best regards,Orly
--
Orly Avraham, Ph.D.Postdoctoral fellowThe lab of Prof. Oded Livnahand the lab
of Prof. Ora Schueler-FurmanThe Hebrew University of JerusalemIsrael
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