[phenixbb] phenix.refine problems with my pdb

Luca Jovine luca.jovine at biosci.ki.se
Thu Mar 15 07:22:07 PDT 2007


Hi Matt,

Waters refine OK (at least in my hands) as long as you stick to this  
format:

ATOM  31567  O   HOH W2244      15.221 -55.194  88.452  0.72  
48.20      W    O

However, I'd be interested to know if the real problem is not your  
ligand(s) after all - because I am having exactly the same issue you  
described when I try to refine some hydrated ions...

Ciao Luca


On 15 Mar 2007, at 15:15, Matthew Bowler wrote:

> 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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb



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