[phenixbb] refinement with a covalent inhibitor.

[Nigel W Moriarty]

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

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