Re: [phenixbb] phenix.refine problem CIF generated by PRODRG

I have seen problems with tye PRODRG cif files as well, mainly due to the presence of 'inconsistent' torsion restraints. If you use elbow.builder , this should not be a problem (and comes with the phenix suite btw) You can feed elbow a smiles string, or (if you don't have that) give it a PDB file. If hydrogens or connect records are there, it will do a good job figuring out what the geometry is/should be. Cheers Peter ----- Original Message ----- From: Lucas Bleicher Date: Thursday, March 15, 2007 7:44 am Subject: Re: [phenixbb] phenix.refine problem CIF generated by PRODRG To: [email protected], PHENIX user mailing list

--- Nicholas Noinaj escreveu:

...

if all else fails, have you tried getting parameters for your ligand from the PRODRG Server and using that for inputing the ligand parameters into phenix.refine directly when you setup the refinement job? (I think i have done this before???) here is the website in case you aren't familiar... http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

The message was not directed to me, but as PRODRG was cited, I'd like to comment on that.

I have been using the PRODRG server to generate parameters for my ligands for some time. When I use the CIF file on refmac it works perfectly. However, if I use the same file on phenix.refine the ligand becomes very distorted. I could do all protein refinement on phenix.refine and then run some cycles of refinement on refmac to do ligand refinement, but I'd really like to do all the refinement in phenix, which, for my cases, seems to produce much better results than refmac. Does anybody faced a problem like this? If so, did you succeeded in correcting it?

Lucas Bleicher

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