[phenixbb] phenix.refine problem CIF generated by PRODRG

Petrus H Zwart PHZwart at lbl.gov
Thu Mar 15 08:48:36 PDT 2007

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.



----- Original Message -----
From: Lucas Bleicher <lbleicher at yahoo.com>
Date: Thursday, March 15, 2007 7:44 am
Subject: Re: [phenixbb] phenix.refine problem CIF generated by PRODRG
To: noinaj at uky.edu, PHENIX user mailing list <phenixbb at phenix-online.org>

> --- Nicholas Noinaj <noinaj at uky.edu> 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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