[phenixbb] phenix.refine problems with my pdb

Pavel Afonine pafonine at lbl.gov
Thu Mar 15 09:29:04 PDT 2007


Hi Everybody,

if you run phenix.refine like:

% phenix.refine data.mtz model.pdb

and it stops with something like:

Sorry: Fatal problems interpreting PDB file: ...

this means there is unknown (to Monomer Library) molecule in you file. 
The standard way to fix it is to get a cif (parameters file) by running 
eLBOW (which is a part of PHENIX and CCI Apps):

% elbow.builder model.pdb --do-all

In this case eLBOW will go though your PDB file and generate a cif file 
for all unknown ligands. The output file will contain all in its name, 
like: elbow.XXX.all.cif.

So next time you run phenix.refine as:

% phenix.refine data.mtz model.pdb elbow.XXX.all.cif.

Also, in your case I'm really interested why water molecules in your 
file were causing the problem. I would really appreciate if you send me 
a couple of lines from your PDB file containing problematic waters, so I 
fix it and it will never happens again.

Yes, you can also remove all waters and ask phenix.refine to build them 
anew; it does a good job on doing so:

% phenix.refine data.mtz model.pdb ordered_solvent=true 
main.number_of_macro_cycles=5

Please let us know if you still have any questions / problems.

Pavel.





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