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Issue with phenix.superpose_maps
by Stephen Graham 03 Dec '10

03 Dec '10

Hi all, I'm trying to use phenix.superpose_maps through the GUI to get superposed maps covering the same region of NCS-related chains A and B for a figure. I have used PDB Tools to split the model into two files with only chain A or chain B. However, when I run superpose_maps specifying the two individual chains for the input PDB files but the same mtz file for the map coefficients I only get one output map (I think it overwrites the output file...). Selected input from the generated .eff file is as follows: input_files { map_1 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz" labels_1 = 2FOFCWT,PH2FOFCWT map_2 = "/home/stepheng/blah/Native_refine_6_map_coeffs.mtz" labels_2 = 2FOFCWT,PH2FOFCWT pdb_1 = "/home/stepheng/blah/Native_refine_6_chainA.pdb" d_min_1 = None pdb_2 = "/home/stepheng/blah/Native_refine_6_chainB.pdb" d_min_2 = None output_dir = "/home/stepheng/blah" } And the end of the output is as follows: saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4 Wrote Native_refine_6_chainA_superposed.pdb Wrote Native_refine_6_map_coeffs_superposed.ccp4 saving CCP4 map to Native_refine_6_map_coeffs_superposed.ccp4 Wrote Native_refine_6_chainB_superposed.pdb Wrote Native_refine_6_map_coeffs_superposed.ccp4 A bug? Stephen P.S. Incidentally, is there any reason you write both maps in a P1 box rather than putting map 2 on top of map 1 in the position of the first (reference) model? The latter would be more convenient as you can then re-use your carefully chosen pymol viewing matrices for all figures... -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638

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question about xtriage
by crystallogrphy 02 Dec '10

02 Dec '10

Hi, I am checking the space group of my data set using phenix.xtriage. However, the program terminated in the following scripts. Does anyone knows why and what should I do? Thanks! phenix.xtriage B13_native.sca Traceback (most recent call last): File "/usr/local/phenix-1.6.4-486/cctbx_project/mmtbx/command_line/xtriage.py", line 20, in <module> xtriage.run(args=sys.argv[1:]) File "/usr/local/phenix-1.6.4-486/cctbx_project/mmtbx/scaling/xtriage.py", line 866, in run output_file = open( params.scaling.input.parameters.reporting.log ,'w') IOError: [Errno 13] Permission denied: 'logfile.log'

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force field of PHENIX.refine ?
by chene＠umbi.umd.edu 02 Dec '10

02 Dec '10

Dear authors of PHENIX, I just want to know what force field is used by phenix.refine, especially for simulated annealing, CHARMM, AMBER, or what else? Thanks. Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122

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distance constrain in phenix
by r n 02 Dec '10

02 Dec '10

Hi I would like to do distance restrain refinement for metal coordination. How can I do metal - protein strict distance restrain refinement in phenix? Thanks ram

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Hydrogen occupancies
by Florian Sauer 01 Dec '10

01 Dec '10

Dear all, I'm currently refining a small protein against 0.96A data using phenix.refine (1.6-486) from the GUI. Refinement without hydrogens yielded Rwork/free of 12.4/14.2. I then added H-atoms with phenix.reduce and switched to individual refinement of hydrogens which dropped the R-factors to 11.3/13.4. After this refinement the occupancies of some hydrogens dropped to 0 which makes me a little concerned. See e.g.: ATOM 752 H LYS A 45 -7.443 2.613 9.537 1.00 4.73 H ATOM 753 HA LYS A 45 -9.707 1.128 9.401 0.55 2.42 H ATOM 754 HB2 LYS A 45 -8.476 2.797 7.435 1.00 10.58 H ATOM 755 HB3 LYS A 45 -9.795 1.948 7.166 0.95 8.70 H ATOM 756 HG2 LYS A 45 -10.840 3.210 8.889 0.00 33.83 H ATOM 757 HG3 LYS A 45 -9.604 4.206 8.775 0.00 33.83 H ATOM 758 HD2 LYS A 45 -11.227 3.615 6.563 0.00 62.10 H ATOM 759 HD3 LYS A 45 -11.508 4.867 7.507 0.00 62.10 H ATOM 760 HE2 LYS A 45 -9.229 5.527 6.985 1.00 83.62 H ATOM 761 HE3 LYS A 45 -9.348 4.488 5.786 0.00 83.86 H ATOM 762 HZ1 LYS A 45 -10.909 5.758 4.853 1.00 99.63 H ATOM 763 HZ2 LYS A 45 -11.131 6.534 6.042 0.35100.44 H ATOM 764 HZ3 LYS A 45 -9.917 6.715 5.257 0.39100.08 H I would like to ask whether it is possible in phenix to group the occupancies to keep them at the same value as the rest of the residue but still refine xyz and isotropic adp of the individual hydrogens? Thank you in advance for your answers, Florian

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wander wall interaction
by subhash bihani 01 Dec '10

01 Dec '10

hi all I am working on a enzyme-ligand complex structure. For some analysis I need to remove wander wall interactions between protein and ligand. How can I do that in Phenix? Something similar to igroup statement in CNS? Thanks in adwance -- Subhash Bihani Scientific Officer Solid State Physics Division Bhabha Atomic Research Centre Trombay, Mumbai-85 Ph. 25594688 (o) alternate email: subhashbihani(a)yahoo.co.in

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phaser and threads
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-595 ] [ GNU/Linux 2.6.31-20-generic #58-Ubuntu SMP four-processors ] [ compiled from source with --no-gui --no-apps --openmp ] i noticed phaser splits the rotation onto 2 threads - just wondering why that might be, since i used nproc=4 on the command line.... oh, hmmm... i seem to have just got this at the packing function : |python: malloc.c:4591: _int_malloc: Assertion `(unsigned long)(size) >= (unsigned long)(nb)' failed. -Bryan

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building from source : svn_checkout
by Bryan Lepore 01 Dec '10

01 Dec '10

[ dev-596 from source using --no-gui --no-apps --openmp ] README-DEV mentions ./bin/svn_checkout ... i cannot find this (but i do find bundle_update and recompile). any pointers appreciated. -Bryan

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Refinement of a complex with a symmetric inhibitor lying on the axis of symmetry
by Ina Lindemann 01 Dec '10

01 Dec '10

Hi, I try to refine a crystal structure of a protein - inhibitor complex. The protein is a homodimer and the two molecules have a crystallographic symmetry. The space group is P6122. The symmetric inhibitor binds symmetrically to the protein so that I refine the half of it. The core of the inhibitor is a five-membered ring with a nitrogen lying directly on the axis of symmetry. I achieved to refine this by setting the occupancy to 1.0. And now, here is my problem: Two C atoms of this ring system are bound across the symmetry axis - how could I include this in the refinement? Is there any possibility to generate restraints to the other part of the inhibitor (of the symmetry equivalent)?? Thanks for your help in advance, Ina Ina Lindemann Philipps-Universität Marburg Pharmazeutische Chemie AG Klebe Marbacher Weg 6 35032 Marburg Tel.: 06421/2825908

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autosol : unmerged data with input_phase_file
by Bryan Lepore 30 Nov '10

30 Nov '10

dev-595 i gather that autosol will not take unmerged data when the input_phase_file originates from merged data. e.g. in "method #2 for MRSAD". -Bryan

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