[phenixbb] refinement with a covalent inhibitor.
Nigel W Moriarty
NWMoriarty at lbl.gov
Tue Mar 17 15:37:22 PDT 2009
Yes, please do download the latest PHENIX version and run ReadySet!
again. To ensure that the ASG-GCU complex is handled correctly, you
should put in the CONECT records into the PDB file that link the two
"residues" in your ligand complex together. This is a rather complex
example and I'd be interested in seeing your PDB file.
On 3/17/09 3:10 PM, Maia Cherney wrote:
> Thank you Nigel,
> However, your cif file did not help with the problem (carboxylate is not
> planar) when using the PHENIX 1.4-3 version that we have now. You
> mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to get
> them both? By the way, phenix.ready_set (in our current version) screwed
> up all hydrogens in my other ligand (trimer of ASG-GCU). I think that
> the ready.set needs to know that the monomers are linked. With this
> particular ligand that is a hexamer, ASG is in the library, but GCU is
> not. Should I give a cif_link file for the ready.set, too? After I get a
> newer version of phenix, I 'll try it again.
> Nigel W Moriarty wrote:
>> 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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
Nigel W. Moriarty
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
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