[phenixbb] refinement with a covalent inhibitor.

Maia Cherney chern at ualberta.ca
Tue Mar 17 15:10:20 PDT 2009

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:
> 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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