December 2011 - phenixbb - phenix-online.org

Re: [phenixbb] Compilation problem rosetta MR on Fedora 10
by Eugene Valkov 15 Dec '11

15 Dec '11

Hi Martin, I had encountered an issue with building Rosetta 3.2.1 on Ubuntu 11.04, specifically that SCons could not compile it because it used gcc 4.1 libraries, whereas there was gcc 4.4 installed. Could you check what version of gcc you have installed on your Fedora box? If it is the compiler issue then there are some workarounds documented on Rosetta forums: https://www.rosettacommons.org/node/2274 These worked for me, but you have to hack around in code a bit to make it happen. HTH, Eugene > On 15 December 2011 13:08, Martin Moche <Martin.Moche(a)ki.se> wrote: >> Dear Phenix Users, >> >> I am trying to compile rosetta mr on my fedora 10 computer: >> http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35 >> >> Compared to the instructions >> % tar xzf rosetta3.2_Bundles.tgz >> >> did not work for me, instead I run >> % tar xvf rosetta3.2_Bundles.tgz >> >> and subsequently >> % tar xvf BioTools-3.3.tgz >> % tar xvf protocol_capture-3.3.tgz >> etc etc >> >> From the rosetta_source directory as an ordinary user (not root) I run: >> % python scons.py -j2 bin mode=release >> >> The compilation runs for a while but finally I got the termination message >> below. >> >> What should I try next? >> >> Best regards, >> Martin >> >> #################### my computer info ################## >> >> daffy-mochma 183% scons --version >> SCons by Steven Knight et al.: >> script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons >> Foundation >> >> daffy-mochma 104% uname -a >> Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST >> 2009 i686 i686 i386 GNU/Linux >> >> daffy-mochma 105% python --version >> Python 2.5.2 >> >> >> >> ############# termination message ############################# >> >> g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so >> -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/ >> -shared >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os >> build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os >> build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os >> build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os >> build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/heap.os >> build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os >> build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/exit.os >> build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os >> -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc >> -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib >> -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3 >> /usr/bin/ld: cannot find -lz >> collect2: ld returned 1 exit status >> scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1 >> scons: building terminated because of errors. >> >> >> Martin Moche, Ph.D. >> Head of Protein Crystallography >> Karolinska Institutet >> MBB/PSF >> Scheeles väg 2 >> 171 77 Stockholm >> Sweden >> phone: +46-8-524 868 43 >> mobile: +46-73-322 93 27 >> fax: +46-8-524 868 68 >> email: Martin.Moche(a)ki.se >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> -- Eugene Valkov, D.Phil. MRC Career Development Fellow Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH email: evalkov(a)mrc-lmb.cam.ac.uk tel: +44 (0)1223 402261

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loosening constraints on water addition
by Crystal VanderZanden 15 Dec '11

15 Dec '11

I'm trying to adjust the parameters on the water picking to allow for more waters to be found. I tried creating a solvent.params file with the code below, then I increased and decreased the primary map cutoff. When I ran the water picking command with the solvent.params file, it actually decreased the number of waters found, both at the high and low primary map cutoff. Does anyone know what I can do to relax the water finding criteria so more waters will be found? Thanks, Crystal refinement { ordered_solvent { low_resolution = 2.8 b_iso_min = 1.0 b_iso_max = 50.0 b_iso = 25.0 primary_map_type = mFobs-DFmodel primary_map_cutoff = 3.0 secondary_map_and_map_cc_filter { cc_map_2_type = 2mFobs-DFmodel } } peak_search { map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 } } }

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how to get the sf.ent file
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, Will you please tell me how can I get the sf.ent file from a PDB enty? Cheers, Dialing

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wilson scale
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, For my structure, the wilson scale is 0.5, is it fine or not? Best regards. Dialing

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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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