[phenixbb] phenix.refine problems with my pdb

[Petrus H Zwart]

Not sure what the exact problem is unless you send a file/line.

IN any case, just delete the waters and add

ordered_solvent=True 

to the command line pick waters and refine them. It works really well.

Peter


----- Original Message -----
From: Matthew Bowler <mwb at mrc-dunn.cam.ac.uk>
Date: Thursday, March 15, 2007 6:16 am
Subject: Re: [phenixbb] phenix.refine problems with my pdb
To: noinaj at uky.edu, PHENIX user mailing list <phenixbb at phenix-online.org>

> Thanks for replies so far....
> 
> I removed all ligands and then waters - the waters seem to be the  
> problem as the protein model is now refining, do they need to be  
> treated/marked in a different way for phenix?
> 
> Thanks again, Matt.
> 
> 
> On 15 Mar 2007, at 13:32, Nicholas Noinaj wrote:
> 
> > matt,
> >
> > can't offer much help, but have you tried to remove the ligand 
> and  
> > try refinement?  it would let you know if the pdb file or the  
> > presence of the ligand is the problem.  at least let you would 
> know  
> > where you should focus your attention.
> >
> > 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/
> >
> > Again, Best of luck!
> >
> >
> >
> > cheers,
> > nick
> >
> >
> > -----Original Message-----
> > From: Matthew Bowler <mwb at mrc-dunn.cam.ac.uk>
> > To: phenixbb at phenix-online.org
> > Date: Thu, 15 Mar 2007 13:00:42 +0000
> > Subject: [phenixbb] phenix.refine problems with my pdb
> >
> > Dear All,
> > 	I am trying to run phenix.refine but I keep getting the message:
> >
> >
> > Sorry: Fatal problems interpreting PDB file:
> >    Number of atoms with unknown nonbonded energy type symbols: 308
> >    Please edit the PDB file to resolve the problems and/or 
> supply a
> >    CIF file with matching restraint definitions. Note that
> >    elbow.builder is available to create restraint definitions.
> >
> > I have run my ligands through elbow and used the output .cif but I
> > still get the same message.  I can find no info on this problem in
> > the manual or the BB, can anyone help?  Thanks in advance, 
> yours,  
> > Matt.
> >
> >
> >
> >
> >
> > Matthew Bowler
> > MRC Dunn Human Nutrition Unit
> > Wellcome Trust / MRC Building
> > Hills Road
> > Cambridge CB2 2XY
> > Tel: 0044 (0) 1223 252826
> > Fax: 0044 (0) 1223 252825
> >
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> >
> >
> >
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> 
> Matthew Bowler
> MRC Dunn Human Nutrition Unit
> Wellcome Trust / MRC Building
> Hills Road
> Cambridge CB2 2XY
> Tel: 0044 (0) 1223 252826
> Fax: 0044 (0) 1223 252825
> 
> _______________________________________________
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