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phenix.superpose_pdbs and nucleic acids.. does it work?
by Francis E Reyes 14 Dec '11

14 Dec '11

Hi phenixer's. I need to do a superposition of two pdbs. I guess phenix.superpose_pdbs is my jiffy but it doesn't seem to work for nucleic acids (tried selection = 'name P' or selection = 'all'). LSQKAB seems to have the same limitation. They are the exact same PDBs (1 to 1 atom/residue mapping) but just shifted and rotated relative to the other. I need a superposition or the transformation matrix for all atoms. Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 450, in <module> run(args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 434, in run m = manager(params.extract(), log) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 171, in __init__ selection_moving = self.selection_moving) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 306, in _alignment "bugs(a)phenix-online.org for help.") RuntimeError: Failed to identify corresponding atoms from sequence alignment. This is probably a bug - contact bugs(a)phenix-online.org for help. I may just strip it down to phosphate's and rename the residues to ALA but a quick phenix jiffy would be great. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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on residue bond deviation
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, After a key step refinement byPhenix refine, I find there are 2 residues (total about 450 residues) with bad angles as analyzed by MolProity (deviation ratio 0.46%, goal is 0.1% ), both of the 2 residues are Pro, and both of the deviation angles are C-N-CA. Will you please give the comment on what do the 2 deviations mentioned above mean for my whole protein structure, or should I continue to refine my protein structure? I am looking forward to getting your reply. Dialing

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on the input file for the Phase and build
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, For the Phenix Phase and build, the input mtz file is the scala mtz file, and the ouput mtz file will be the mtz file with phase, is this correct? I am looking forard to getting a reply from you. Cheers, Dialing

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strange MR problem
by intekhab alam 13 Dec '11

13 Dec '11

Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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Phenix version 1.7.3 released
by Paul Adams 13 Dec '11

13 Dec '11

The Phenix developers are pleased to announce that version 1.7.3 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: MR-Rosetta - viewer for diffraction images (also available as phenix.image_viewer) - editable heavy-atom sites in HySS and AutoSol General: ======== - New commands: phenix.ncs_average, phenix.model_vs_sequence, phenix.image_viewer, phenix.find_alt_orig_sym_mate, phaser.MRage - support for CNS v1.3 reflection files Refinement: =========== - Reduced memory requirement for map related calculations - Improved handling of parameter files in the GUI - RNA geometry target now includes pucker & base type-specific Chi 1 parameters - TLS group definitions from PDB file header will be automatically used if no groups are provided by the user - Bug fix in clashscore calculation for large structures with duplicate chain IDs plus SEGIDs - Torsion NCS restraints uses SEGIDs if present in input PDB file Molecular Replacement: ====================== - phaser (version 2.4): - support for pseudo-translational non-crystallographic symmetry (tNCS) in molecular replacement - detects presence of tNCS from inspection of native Patterson - characterizes tNCS parameters (translation, small rotational difference between copies) - accounts for effect of tNCS in molecular replacement calculations - note: support currently limited to one tNCS operator relating two molecules (or sets of molecules) - FAST search method turned on by default, replacing FULL search method - MR possible with a model containing a single atom - B-factor refinement turned on by default in molecular replacement - Bug fix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux - Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position - phaser.MRage (version 0.1.0) - automated MR: - New command-line switches for common actions, e.g. setting the verbosity, getting PHIL parameters, etc - Define component by sequence, but calculate molecular weight from available models if sequence is omitted - Calculate number of copies to find from Matthews coefficient - Ability to perform homology search (currently only BLAST is supported, either local installation or NCBI service) - alignments automatically generated for "template" if target sequence is known - various options for queueing systems, e.g. qslot - option to automatically write out solutions - fully parallel space group exploration - phenix.find_alt_orig_sym_mate (new command): - For different molecular replacement solutions from the same dataset, finds the copy of moving_pdb closest to reference_pdb with respect to all symmetry operations and alternative origin shifts permitted by the spacegroup in moving_pdb Experimental Phasing and Model Building: ======================================== - AutoSol: - Fixed problems with clean_up=True deleting overall_best.pdb - Allow data file names of any length - Use NCS in scoring by default if ncs copies > 2 - Correct anisotropy and sharpen by default - AutoBuild: - Automatic anisotropy correction and sharpening for all maps - phenix.multi_crystal_average: - Automatic anisotropy correction and sharpening - Automatic filling of reflections to highest resolution of any dataset - Masking heavy-atom sites from averaging - Inputs grouped by crystal Miscellaneous: ============== - phenix.ready_set/phenix.reduce: - Improved handling of alternate conformations - phenix.cif_as_mtz - Support for files containing multiple datasets - Extraction of Hendrickson-Lattman coefficients and anomalous arrays - New map_to_asu and remove_systematic_absences options - phenix.maps: - Added atom selection parameter for simple omit maps (omit.selection) - phenix.ligand_identification: - Implemented methods to generate custom ligand library based on parent protein's SCOP or CATH terms, Pfam accession numbers, GO accession numbers, or InterPro ID - Improved ligand geometry after real-space refinement For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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ncs_average output map
by Ursula Schulze-Gahmen 12 Dec '11

12 Dec '11

I am puzzled about my ncs-averaged output map. I determined the ncs relation using phenix.find_ncs with pdb and mtz input. The program finds 2 NCS groups with 3 molecules each and the rmsds are low. I then read in the ncs_spec file and an mtz file with map coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT coefficients. The output map seems cleaner than the unaveraged map and shows some of the same features, but the density around the 3 molecules is not identical. 2 of them look very similar, but the density around one of them is somewhat different. How is this possible if the map is averaged? Thanks for any suggestions or explanations. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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AutoBuild Question
by Page, Rebecca 12 Dec '11

12 Dec '11

Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca

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phenix.refine_failed
by Xue-Yuan Pei 12 Dec '11

12 Dec '11

Dear Phenix Experts: My phenix.refine has developped the following error (see below). I tried to check my PDB format, there is not B-factor error. so what could be wrong that stoped my phenix.refine without PDB and .def files in the output? Many thanks for your advice. Xue yuan Pei, Ph.D Department of Biochemistry University of Cambridge Cambridge CB2 1GA U.K > Error messages: > Traceback (most recent call last): > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", > line 105, in run > refine_object.write_refined_pdb(f_pdb) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", > line 1284, in write_refined_pdb > ignore_hd = not self.neutron_refinement) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 534, in __init__ > ignore_hd = ignore_hd) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 449, in __init__ > molprobity_scores=True) > File "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model.py", > line 1063, in geometry_statistics > molprobity_scores = molprobity_scores) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 112, in __init__ > self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/validation/clashscore.py", > line 167, in analyze_clashes > stdin_lines=tmp_r.as_pdb_string()) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/iotbx/pdb/hierarchy.py", > line 527, in as_pdb_string > siguij=siguij) > RuntimeError: atom B-factor does not fit into F6.2 format: > "ATOM 1 N GLY A 1 " > B-factor: 111147.29 >

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phenix.refine_failed
by Christian Roth 12 Dec '11

12 Dec '11

Hi, indeed your B-Factor shown in the error message for Gly A 1 is unrealistic. Is maybe in your pdb-file a space missing? I think a 8 digit B-Factor is not possible in the pdb format. Best Regards Christian

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Phaser not writting out ligands
by Yarrow Madrona 09 Dec '11

09 Dec '11

Hello, I am having trouble with Phaser not writing out my ligands (HEME and small molecule) to it's output PDB even though they are in the input PDB. I am running through the GUI using Phenix version 1.7.3-921. Phenix refine recognizes HEME from the CCP4 library I think so I am not sure why I at least do not get a HEME in the output PDB. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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