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Rosetta_refine stuck...?
by Jan Gebauer 09 May '14

09 May '14

Hello everyone, First of all thanks to the developers for improving the installation of rosetta_refine. In contrast to my experiences half a year ago, this time the installation was easy and straightforward. However, refining a 600 Aa @ 3.5 A with 4 mol per asu one more than one processor still completely breaks my computer. (Intel i5 2500K / 7.8 GB RAM) I think this might be a memory issue. Having only a "normal" PC, one process already uses 5GB of RAM which equals 60% of my RAM. With only one process running the first of five model was finished in roughly 3 hours. However, the second model already takes more than 10 hours, and the log file on the _ros_tempXXX file wasn't update for the last 9 hours. I can't see any progress, however it still uses 100% of one processor. Unix's top tells me that "reduce" is completely using this resource and that it had run for the last 821 minutes... so I guess rosetta_refine is somehow stuck? Any ideas why it is stuck and how to solve that? With kind regards, Jan Gebauer By the way: Is rosetta_refine meant to work on a "normal" Computer - like mine. In principle I would have access to a cluster, but set-up time there would be considerably long for me... -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066 http://px.uni-koeln.de/

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FEM mtz won't open in coot
by de Waal, Parker 09 May '14

09 May '14

Hello Everyone, I'm having trouble opening the map file generated by phenix.fem in coot. Each time I try and load the .mtz file the follow error occurs 'Failed to find any suitable F/phi columns in the MTZ file'. Dumping the mtz file I can see: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE 0 33 0 100.00 12.1 12.1 114.15 3.31 H H 2 NONE 0 33 0 100.00 12.8 12.8 114.15 3.31 H K 3 NONE 0 137 0 100.00 51.4 51.4 114.15 3.31 H L 4 NONE 0.0 10551.1 22963 71.24 406.13 406.13 39.60 3.31 F 2mFoDFc 5 NONE -180.0 180.0 22963 71.24 0.98 89.81 39.60 3.31 P PHI2mFoDFc 6 NONE 5.2 51589.8 0 100.00 1602.72 1602.72 114.15 3.31 F FEM 7 NONE -180.0 180.0 0 100.00 0.32 89.74 114.15 3.31 P PHIFEM If someone could help me to rename these columns to a coot friendly format so that I would be greatly appreciative. Best, Parker

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PHENIX.apply_ncs question
by Sun Bingfa 07 May '14

07 May '14

Hi guys, I've been working on a structure using NCS. When I run the phenix.apply_ncs to generate the whole structure using the original one chain PDB, it gave me a PDB with same atom number on the other chain. For example, I start with chain A and end in chain A and B (B is generated by NCS), while the atom number on chain B is just a duplicate of chain A, starting from 1. This cause error in the subsequent refinement trials. I'm wondering what program can correct this issue. Thanks, Bingfa

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PHENIX-Coot problem
by Marcelo Carlos Sousa 07 May '14

07 May '14

I recently updated to CCP4 6.4 including Coot. I updated the path in phenix to point to the coot wrapper startup script. Phenix then correctly starts Coot and both programs are "connected". However regularizations or real space refinement fail with the "Failed to find restraints for: …" message as if the dictionaries are not loading. This does not happen when starting Coot from the terminal or form CCP4i… Any ideas on how to solve this problem? ____________________________________________ Marcelo C. Sousa, Ph.D. Associate Professor Department of Chemistry and Biochemistry University of Colorado at Boulder 596 UCB Boulder, CO 80309 Phone: (303) 735 4341 Fax: (303) 492 8425

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Making beautiful crystallographic maps with FEM (Feature Enhanced Map) - new Phenix tool
by Pavel Afonine 07 May '14

07 May '14

Dear Phenix users, this is a quick announcement of a new Phenix tool to improve crystallographic maps. Link below provides most information: from method overview and examples to usage details: http://www.phenix-online.org/presentations/fem_06MAY2014.pdf Should you have any questions, bug reports or any other feedback *please send it to me directly*. All the best, Pavel

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LAST DAY TO REGISTER: SBGrid/NE-CAT Computing School
by Michelle Ottaviano 07 May '14

07 May '14

We're in the final stages of planning for our June Computing School and *registration will close on Friday. *Join us in June for our data processing workshop followed by Phenix and Schrodinger/BioLuminate workshops. *Register Here <http://www.events.harvard.edu/profile/web/index.cfm?PKWebId=0x12902a67d>: Deadline Friday, May 9th* *Quo Vadis Structural Biology 2014* SBGrid/NE-CAT Computing School June 5-7, 2014 Harvard Medical School -- Boston, MA *Data Processing in Crystallography - June 5-6:* Speakers: Kay Diederichs, Phil Evans, Zbyszek Otwinowski, Jim Pflugrath, Dominika Borek, Piotr Sliz, Matt Benning, , Frank Murphy, David Neau, K. Rajashankar, Nick Sauter, Jon Schuermann, Clemens Schulze-Briese *Advances in Structure Determination with Phenix - June 7:* Paul Adams & Nathaniel Echols, Lawrence Berkeley National Laboratory Tom Terwilliger, Los Alamos National Laboratory *Improved Structural Modeling Using BioLuminate - June 7: * Melissa Landon, Ph.D., Schrodinger, Inc. Complete meeting details can be found here: https://sbgrid.org/news/sbgridne-cat-computing-school

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Occupancy refinement troubles
by Kieft, Jeffrey 07 May '14

07 May '14

Hello All, Question about occupancy refinement. I'm refining an RNA structure at 2.0 Angstrom resolution with bound ligands iridium hexammine and spermine. The location of the former can be confirmed in an anomalous difference map, but they are likely not full occupancy...likewise the spermine is likely less than one. When I use occupancy refinement, it leaves the RNA at full occupancy as expected, but refines each atom of the irhex and spermine individually, in some cases driving the occupancy to 0 for some atoms. It seems like this was an issue in the past, but I'm still seeing it. Any ideas? Could if be that Phenix doesn't recognize those ligands? Parameter files wrong? Thanks for help! Jeff

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Current version download
by Marcelo Carlos Sousa 06 May '14

06 May '14

I was checking for the current official Phenix release and the website lists 1.9-16090. However, upon downloading it seems to be 1.8.4-1496… Am I doing something silly? Marcelo

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Geometry regularization in phenix.pdbtools
by Francis Reyes 06 May '14

06 May '14

Hi all, I always enjoyed geometry regularization in phenix.pdbtools. Has it been moved elsewhere? phenix.pdbtools file.pdb --geometry-regularization ceases to exist . Thanks, F

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Phenix-rosetta refinement problems
by Oliver Clarke 05 May '14

05 May '14

Hi all, I am struggling a little to get Rosetta and phenix to play happily with one another (I’d like to use the phenix.rosetta_refine module). I am currently using the latest nightlies of phenix (1.9-1690) and rosetta (2014.16.56682), and I run into errors (reproduced below) when attempting to build the phenix-rosetta interface. Does anyone have any insights as to how to fix this problem, or suggestions as to which pair of phenix and rosetta versions are known to be compatible with one another? Many thanks, Oliver. Errors while building phenix-rosetta interface: <snip> chdir(tempdir_.c_str()); src/core/scoring/cryst/PhenixInterface.cc:375:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::string)': src/core/scoring/cryst/PhenixInterface.cc:949:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1075:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1095:25: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1104:13: error: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Werror=unused-result] chdir(".."); ^ g++ -o build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/MinimizationGraph.os -c -std=c++98 -isystem external/boost_1_55_0/ -isystem external/include/ -isystem external/dbio/ -pipe -ffor-scope -Wall -Wextra -pedantic -Werror -Wno-long-long -Wno-strict-aliasing -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/MinimizationGraph.cc cc1plus: all warnings being treated as errors scons: *** [build/src/release/linux/3.11/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors.

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