[phenixbb] refinement with a covalent inhibitor.
Nigel W Moriarty
NWMoriarty at lbl.gov
Tue Mar 17 12:09:46 PDT 2009
Maia
Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar groups
including the carboxyl group missing from the earlier PHENIX version I
believe you used. I have attached it. There are a few other things I
should mention.
I used a tool called ReadySet!
phenix.ready_set model.pdb
which will generate (using eLBOW) CIF files for all the ligands in the
model using the data from the Chemical Components database from the
PDB. I would recommend that you use ReadySet! for preparing a PDB file
for refinement. It also adds hydrogens to your model which is usually a
good thing.
Your example does have some nuances. You mention that it is covalently
bound to the CYS. I have attached the two additional files needed to
inform phenix.refine of the covalent bond. I used eLBOW directly for
this but will ensure that ReadySet! will do the same function in the
next release.
An additional function that I have been working on recently is the
removal of the hydrogen in a carboxyl group when the ligand is in the
model. I shall have that in the next PHENIX release.
Finally, I did a refinement using dummy reflection data and the carboxyl
group remained planar.
If you have any problems with any of the files, feel free to contact me
directly.
Nigel
--
Nigel W. Moriarty, Ph.D.
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: e64_cys.mod_links.cif
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090317/af1a318a/attachment-0003.el>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: e64_cys.def
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090317/af1a318a/attachment-0004.el>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: e64.cif
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090317/af1a318a/attachment-0005.el>
More information about the phenixbb
mailing list