[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.
> Maia
> Nigel W Moriarty wrote:
>> 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
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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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