Dear Elke,
That seems to have done the trick. Can't thank you enough!!! I'm so happy.
For future readers:
ca6 alt loc A and residue 401 70% occ
pa3 #1 alt loc B and residue 402 30% occ
pa3 #2 alt loc C and residue 403 30% occ
I could have probably done pa3 #1 and #2 as the same residue 402 as I
d7-dmarc-requ...@jiscmail.ac.uk>
À: "CCP4BB"
Envoyé: Jeudi 16 Février 2023 18:40:31
Objet: Re: [ccp4bb] Refinement of ligand with alternate chemical structure
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 molecul
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
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
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 : nw
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 <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
> I fit a large cyclic ligand cA6 (cylic hexa-adenylate) and after some
> refine
Hi Stuart,
the answer, I think, is here:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12
Pavel
On Wed, Feb 15, 2023 at 8:37 AM Stuart McQuarrie <
974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk> wrote:
> I fit a large cyclic ligand cA6 (cylic hexa-a
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
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