Happy New Year indeed. Thank you.
If this is not just a personal programming exercise, Orly Avraham might
also take a look at PISA, python-mmdb and/or gemmi.
Paul.
On 10/01/2020 21:48, Jonathan Cooper wrote:
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 fellow
The lab of Prof. Oded Livnah
and the lab of Prof. Ora Schueler-Furman
The Hebrew University of Jerusalem
Israel
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