Dear all,
I looked at the atom table (atom_site) in the NextGen archive. It has 5 new
columns: pdbx_label_index (another sequence ID) and four columns for SIFTS
mapping at atom level.
I used SIFTS in the past and having it in the coordinate file can simplify
things. But as was stated in the announ
Hi Michael,
I recently installed panDDAs on an older Linux system. It still runs Centos
7, which was nice since I've run into compatibility issues with
python3/python 2.7 on a newer Mac.
Here are the basic steps that I've had to follow:
--Install cpp4 7.0 and download the updates to get to the ri
Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of
the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC .
It notes these atoms are too close but carries on refinement happily
enough..
But when I read the structure into COOT and try to refine the A copy
Stuart
The sum of occ in these three is 1.3 and it looks like you put the occ in
the B-factor column.
Cheers
Nigel
---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : nwmoria...@lbl.gov
Web
Dear everyone that replied, thanks so much for the help thus far.
Just for info I’m using Coot for Windows version 0.9.6 EL and phenix.refine
version 1.20rc4-4416-000
RE Eleanor: It appears my version of coot/refmac do not support separate
ligands in the same space at <0.5 occupancy. As an ex
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Hi Pat
There may well be issues with the latest xquartz (2.8.3+) as the libcairo
compatibility version has changed to 1 from being 11 thousand odd. This means
that anything built against an older installation will fail. The workaround
is to use an older xquartz, such as 2.8.0.
That prett
Hi everyone,
I’ve been putting off upgrading to Mac OS 13 Ventura, but my computer is
getting more and more pushy in its demands for a new OS.
Hence I ask, What’s the current status of coot running on Ventura? I’m aware of
the issues that have been discussed in this forum, but that thread seems
Hi Michael
New version coming on Friday. Should fix the issues.
You will be able to upgrade using ccp4um
Sorry for the issues
Charles
From: CCP4 bulletin board on behalf of Michael Weyand
Date: Thursday, 16 February 2023 at 07:30
To: ccp4bb
Subject: [ccp4bb] CCP4 8.0.008 Python2 <-> 3 pro
