[phenixbb] refinement error with ligand

Tom Huxford thuxford at sciences.sdsu.edu
Wed Feb 17 08:12:42 PST 2010


Here is an interesting discussion on ligand refinement in PHENIX

Tom Huxford.

On Feb 17, 2010, at 7:49 AM, Pavel Afonine wrote:

> Hi Christian,
>
> a possible solution using the command line:
>
> 1) take your PDB file with all the ligands,
>
> 2) create a CIF file:
>
> phenix.ready_set model.pdb
>
> 3) edit *.eff file to specify correct input file names for model,  
> data, CIF file (and other parameters if necessary) and run  
> phenix.refine as following:
>
> phenix.refine my_file.eff --overwrite
>
> If it still give you that error message then you may need to send us  
> your PDB file so we can fix the problem. Meanwhile you can try running  
> your refinement without H atoms:
>
> - remove H:
>
> phenix.reduce model.pdb > model_noH.pdb
>
> - run refinement as above.
>
> Pavel.
>
>
>
> On 2/17/10 8:58 AM, Christian Roth wrote:
>> Dear all,
>>
>> I started a refinement of one of my structures using the GUI of  
>> phenix (Version 1.6). I used the options of adding hydrogens and dis  
>> a suimulated annealing. I used the output file and corrected it  
>> manually using Coot. I incorporated a few Ethylenglycol Monomers  
>> which might have bound.  I merged everything wrote the file out  and  
>> loaded this pdb in the GUI. I got an error which might be du to the  
>> fact that I didnt specify a CIF file for the ligand. I started ready  
>> set from the GUI to check the pdb and used REEL to create a CIF File.  
>> I added the CIF-File to the  File list and tried to start again  
>> phenix.refine using the hydrogen option but no sim. annealing.  
>> However I got always the following error log:
>>
>> # Date 2010-02-17 Time 12:00:35 CET +0100 (1266404435.31 s)
>> #phil __OFF__
>>
>> Command line arguments:  
>> "/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/ 
>> refine_15.eff" "--
>> overwrite"
>>
>> HOST = bbzws339
>> HOSTTYPE = i486-linux
>> VENDOR = intel
>> USER = roth
>> PID = 29983
>>
>> ---------------------------------------------------------------------- 
>> ---------
>>   PHENIX: Python-based Hierarchical ENvironment for Integrated  
>> Xtallography
>>   Version: 1.6
>>   Release tag: 289
>>   Platform: intel-linux-2.6 linux
>>   User: roth
>> ---------------------------------------------------------------------- 
>> ---------
>>
>>               phenix.refine: Macromolecular Structure Refinement
>>
>>  Monomer Library directory:
>>     "/software/linuxsoft/phenix-1.6-289/chem_data/mon_lib"
>>   Total number of atoms: 16881
>>   Number of models: 1
>>   Model: ""
>>     Number of chains: 19
>>     Chain: "A"
>>       Number of atoms: 1575
>>       Number of conformers: 1
>>       Conformer: ""
>>         Number of residues, atoms: 94, 1575
>>           Classifications: {'peptide': 94}
>>           Modifications used: {'COO': 1, 'NH3': 1}
>>           Link IDs: {'PTRANS': 6, 'TRANS': 87} and so on for other  
>> chains
>>  Chain: "R"
>>       Number of atoms: 7
>>       Number of conformers: 1
>>       Conformer: ""
>>         Number of residues, atoms: 1, 7
>>           Unusual residues: {'EDO': 1}
>>           Unexpected atoms: {'EDO,HO1': 1, 'EDO,HO2': 1}
>>           Classifications: {'undetermined': 1}
>>   Number of atoms with unknown nonbonded energy type symbols: 16
>>     "HETATM16821  HO2 EDO K   1 .*.     H  "
>>     "HETATM16826  HO1 EDO K   1 .*.     H  "
>>     "HETATM16828  HO2 EDO L   1 .*.     H  "
>>     "HETATM16834  HO1 EDO L   1 .*.     H  "
>>     "HETATM16836  HO2 EDO M   1 .*.     H  "
>>     "HETATM16840  HO1 EDO M   1 .*.     H  "
>>     "HETATM16842  HO2 EDO N   1 .*.     H  "
>>     "HETATM16848  HO1 EDO N   1 .*.     H  "
>>     "HETATM16850  HO2 EDO O   1 .*.     H  "
>>     "HETATM16857  HO1 EDO O   1 .*.     H  "
>>     ... (remaining 6 not shown)
>>
>> I looked in the pdb for this atoms, but I cannot find them.
>> When I use a cif file created directly by phenix elbow using command  
>> line and when I did not use the update hydrogen button the refinement  
>> works. But the new residues as well as the EDO molecules have no  
>> hydrogens in riding positions. Do I have to remove all hydrogens and  
>> attach them again for every cycle?
>> One Refinement runs for more then 5 hours regardless I use sim  
>> annealing or not. This seems to be very long for me. Maybe I want   
>> too many optimization steps?
>>
>> Could anyone explain me what goes wrong here. I am no so much  
>> experienced with phenix and now I run out of ideas.
>> Thanks in advance
>> Christian
>>
>>
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>>
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----------------------
Tom Huxford.
Structural Biochemistry Laboratory
Department of Chemistry & Biochemistry
San Diego State University
(619) 594-1606




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