[phenixbb] refinement error with ligand

[Nigel W Moriarty]

Christian

If you run ReadySet! from the GUI, the output from ReadySet!, 
model.update.pdb which contains the hydrogens may be automatically used 
in the refinement.  You can check by looking in

/homes/roth/clcf/049b32mlsyncref/phenix/phenix/project_data/refine_15.eff

There are restraints for EDO on the monomer library so I'm not sure why 
there is a problem.  I can take a look if you send it directly to me.

The refinement is 1.6-289 can be slow if you have the rotomer fixing 
option set.

Nigel

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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>
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax   : 510-486-5909
Email : NWMoriarty at LBL.gov
Web   : CCI.LBL.gov