[phenixbb] refinement with a covalent inhibitor.

Maia Cherney chern at ualberta.ca
Wed Mar 18 08:34:02 PDT 2009

Hi Nigel,
I can't find the newer phenix versions on the phenix home page. The 
latest version there is the same as I have now, 1.4-3!
Where can I find the newer versions and why they are not on the phenix 
home page?

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