Dear Eleanor,
setting occupancies of omitted atoms to zero has the danger of leaving a
hole with the shape of these atoms in the bulk solvent mask, leading to
positive difference density just because of the missing bulk solvent
density. Since the days of X-PLOR, I always removed the omitted atoms. I
never tried this with REFMAC5, though.
Cheers,
Dirk.
On 07.04.21 11:46, Eleanor Dodson wrote:
Well - I use COOT for this sort of task, and dont trust the automated
tools.
my procedure is
load COOT - probably after a refinement cycle
set occupancy of ligand(s) to 0.00 ( Measures - residue information -
change occupancy)
Look at the environment critically . eg if an ARG or other bulky side
chain nearby , or waters etc selectively set occupancies to 0.00
Doo some more cycles of refinement with this coordinate set to remove
any memory of the ligand.
Look at the map - if the ligand and other zero occ atoms is still in
the right place reinstate them, or try to reinterpret density..
Eleanor
On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund <bjarte.l...@uit.no
<mailto:bjarte.l...@uit.no>> wrote:
Dear Hari,
With regards to 1) Is 15 the number of atoms in your molecule? Or
is it the number of hydrogens? The CIF file may have the wrong
residue name or lack the hydrogens depending on how you built the
ligand-protein complex.
There is also a phenixbb for phenix questions,
http://www.phenix-online.org/mailman/listinfo/phenixbb
<http://www.phenix-online.org/mailman/listinfo/phenixbb>
Kind regards,
Bjarte Aarmo Lund
Postdoc
UiT The Arctic University of Norway
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> *On Behalf Of *Hari shankar
*Sent:* Wednesday, April 7, 2021 08:47
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] Omit maps in phenix and ccp4
Dear All,
I have a ligand-protein complex and I wish to calculate different
kinds of omit maps (say, composite omit maps, simulated annealing
maps, other unbiased fo-fc maps ). I wish to omit the ligand and
3.5 angstrom 3D space around it. I have tried phenix for this
purpose but get this error message consistently.
"Fatal problems interpreting model file: no of atoms with unknown
nonbonded energy type symbols: 15 Please edit the model file to
resolve the problems and/of supply a CIF file with matching
restraint definitions, along with apply_cif_modification and
apply_cif_link parameter definitions if necessary."
This error occurs despite supplying the CIF file for the ligand. I
have tried to remake the CIF/PDB files from SMILES strings, by
drawing the molecule in both ccp4 (acedrug) as well as phenix
(elBOW and Readyset go). Nothing seems to work.
1. Is there something I have missed out that can solve this issue?
2. Is there a program in CCP4i that can be used to generate the
required omit maps?
3. In general, how do I omit 3.5 ang of the space around the
ligand during this map calculations?
Thank you so much for your time.
Hari
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
--
*******************************************************
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
*******************************************************
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
