Dear Stuart,
you have to add
allow_duplicate_sequence_numbers()
to $HOME/.coot.py in OSX or the appropriate place on Windows. For
Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/
directory for configuration - these can be found (added to) the
directory in which Coot was installed (e.g. C:\WinCoot).
Try with crambin (pdbcode 1EJG).This should give an error without
allow_duplicate_sequence_numbers() but coot should start when added.
Br, Georg.
Am 15.02.2023 um 21:47 schrieb Nigel Moriarty:
One may need to set a preference in Coot to allow such a situation to
be viewed. Paul helped me but I can't find the email.
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 : CCI.LBL.gov <http://CCI.LBL.gov>
ORCID : orcid.org/0000-0001-8857-9464
<https://orcid.org/0000-0001-8857-9464>
On Wed, Feb 15, 2023 at 12:37 PM Eleanor Dodson
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
I thought that REFMAC tolerated dual occupancies if the sum of the
two conformers was <= 1.0?
Eleanor
Will test..
On Wed, 15 Feb 2023 at 16:37, Stuart McQuarrie
<0000974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and
after some refinement have noticed partial occupancy of it's
hydrolysed form 2x A3, which has a cyclic 2'-3' phosphate on
the terminal ribose.
I tried fitting both ligands with 50% occupancy, but
refinement doesn't allow them to occupy the same space.
I subsequently tried text editing the pdb file, adding altloc
identifiers to the ca6 and the 2 A3 molecules, making sure
they were same chain and residue number as per this ccp4bb
archive:
http://www.phenix-online.org/pipermail/phenixbb/2011-March/016768.html.
However, before I refined I checked in coot and all the ligand
atoms are scattered and disconnected.
I have thought about using coot to generate an alt
conformation of ca6 and then text editing the B conformation
to be split and have a 2'-3' cyclic phosphate. I am not sure
if this is the correct way because it is a different chemical
structure, so I could use some advice.
Kind regards,
Stuart
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