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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