I wrote a script for auto-generating occupancy refinement relationships
for refmac. It is perhaps not as sophisticated as what phenix does
internally, but it gets common things right, like if you have a 2-headed
side chains or partial-occupancy metals.
https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com
It is a csh/awk shell script. You run it with the name of your input pdb
file on the command line and it dumps the refmac keywords to a file
called refmac_opts_occ.txt and to the terminal. If you want every
"hetatm" atom to be refined put "allhet" as a second command-line argument.
You can then perhaps copy-and-paste this to the relevant GUI window.
-James Holton
MAD Scientist
On 6/7/2021 3:35 AM, Marina Gárdonyi wrote:
Hi,
I didn't know that I can also enter keywords without a file! That is a
good note, thank you!!
Best regards,
Marina
Zitat von Jon Cooper <jon.b.coo...@protonmail.com>:
Hello, the keywords can be entered in refmac gui (in one of the
dropdown things), so you don't need a file, as such, but it's useful
to keep a record.
Sent from ProtonMail mobile
-------- Original Message --------
On 5 Jun 2021, 16:39, Marina Gárdonyi wrote:
Hello everyone,
I am trying to refine structures with Refmac.
The problem is that nobody from my working group is familiar with this
programm. They are using Phenix exclusively.
That's why I need your help. I would like to refine the occupancy. I
know that I need a keyword file for this, but I have no idea how to
create such a keyword file.
Can someone maybe send me a sample file? I think that would help me. I
have found essential keywords, but I don't know how to build up such a
file.
Thank you very much in advance!
Best regards,
Marina
--
Marina Gárdonyi
PhD Student, Research Group Professor Dr. Klebe
Department of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6, 35032 Marburg, Germany
Phone: +49 6421 28 21392
E-Mail: marina....@pharmazie.uni-marburg.de
http://www.agklebe.de/
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