[phenixbb] refinement error with ligand
Nigel W Moriarty
NWMoriarty at lbl.gov
Wed Feb 17 08:37:35 PST 2010
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
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