November 2016 - phenixbb - phenix-online.org

Cannot compile rosetta interface Centos 7 with 1.11.1
by ludovic Pecqueur 21 Apr '17

21 Apr '17

Dear Phenix developers, I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602 When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors). When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors. If you have any idea of the change between the two versions leading to this issue. Thank you for your help, Ludovic. ######################## Error message: Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source ~> phenix.python scons.py bin mode=release extras=python -j 8 scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -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 -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -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 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -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 -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -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 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -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 -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -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 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -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 -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -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 -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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Scale and merge multiple data sets
by Sam Tang 05 Feb '17

05 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

4 5

Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density
by Andrew Morin 30 Nov '16

30 Nov '16

Hello, I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min. For example: I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc. Might anyone know of a handy way to automate this over a large number of mtz files? ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work. Thanks for your help. -Andrew

5 5

Refine only selective chains in a complex using phenix.real_space_refine
by #AHMED TOFAYEL# 30 Nov '16

30 Nov '16

Dear all, Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex. During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line. Best regards, Tofayel NTU Singapore

2 2

Can't Run Rosetta_refine
by NISHANT SINGH 29 Nov '16

29 Nov '16

Hi Everyone, I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done: scons: done building targets. but I am failing at running: rosetta.build_phenix_interface. It says that command not found. I am attaching my env page with this email. bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$

2 1

kickmaps
by Veronica Fiorentino 26 Nov '16

26 Nov '16

Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy Am I missing something obvious? Alternately, If anyone can share a script I would prefer it! many thanks Veronica

3 4

ensemble refinement crash.
by Rajendra Sharma 24 Nov '16

24 Nov '16

Dear all, I am running ensemble refinement using phenix-1.10. The calculations are running good until the Ensemble reducer where the jobs get killed in some cases automatically without giving output pdb. I am using default setting to run the jobs. pdb_stored_per_block is 50 totaling 500 towards the end. Is the crash happening because of memory? Will reducing the number of pdb per block help? Secondly, how can I restart the killed runs? thanks in advance. Raji *Rajendra SharmaResearch Scholar, PhD.* *Centro Nacional de Biotecnología <http://www.cnb.csic.es/>,* *Universidad Autónoma de Madrid,* *Madrid, Spain.Mobile No. +31-656688390*

2 2

Realspace refinement
by Reza Khayat 23 Nov '16

23 Nov '16

Hi, Does realspace refinement consider temperature factors during refinement? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Postdoctoral positions at the NIH in structural and mechanistic studies on integral membrane proteins
by Anirban Banerjee 19 Nov '16

19 Nov '16

Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based biochemistry, electrophysiology together with synthetic chemistry to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or insect/mammalian expression systems will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests.

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 19 Nov '16

19 Nov '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the January 2017 issue is 15 December 2016. However, if you have a brilliant idea during your holiday break please don't hesitate to forward it. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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