April 2017 - phenixbb - phenix-online.org

TLS refinement
by Reza Khayat 02 May '17

02 May '17

Hi, I'm having difficulty with performing TLS refinement on a highly symmetric system. The difference between the R_work and R_free increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The TLS tensors for some of the group are not sensible (if I understand the literature correctly) -there are some negative numbers for the T and L tensors (see below). The TLS groups were identified with phenix.find_tls_groups. Any suggestions would be appreciated. REMARK 3 SELECTION: chain 'A' and (resid 38 through 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.6459 -23.5648 -59.0695 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.2895 REMARK 3 T33: 0.0962 T12: 0.0829 REMARK 3 T13: 0.0473 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0446 L22: 0.0120 REMARK 3 L33: 0.0096 L12: 0.0246 REMARK 3 L13: 0.0209 L23: 0.0106 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.0268 S13: -0.0023 REMARK 3 S21: -0.0507 S22: 0.0526 S23: -0.0287 REMARK 3 S31: -0.0296 S32: -0.0137 S33: 0.0534? The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

2 1

FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 29 Apr '17

29 Apr '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

2 1

radiation damage-induced phasing (RIP) tutorial
by Murpholino Peligro 28 Apr '17

28 Apr '17

Hi lads... Do you know if there is a good tutorial for doing RIP somewhere on the internet? What programs can do RIP? -SHELX -AutoRickShaw -? Thanks

1 0

Can I use PHENIX "Find NCS" tool to verify space group ?
by Alex Lee 23 Apr '17

23 Apr '17

Hi All, I have a protein/dna dataset (3A resolution) with space group (SG) ambiguity, it could be P32 with two copies of molecules (one copy of molecule composed of protein homodimer with asymmetric dsDNA) in asymmetric unit (ASU) or P3221 with one copy of molecule in ASU. Both SG can give me MR solutions and after Refmac P32 Rfree is around 31% while P3221 Rfree is around 34% (without any twin refine at this stage). Density maps from both SG makes sense and they are similar by eye inspection. Because of partial twinning of the dataset (estimation twin fraction alpha around 0.22) , which confuse programs of assigning the correct SG. Pointless and Xtriage suggests P6222, which we are sure it's not correct (based on performance on both MR, Refmac and biology sense that dsDNA is asymmetric, and if P6222 is true then based on Mathew coef. there will be a monomer protein with single strand ssDNA in ASU). Zanuda suggests SG P32 in both cases (input experimental data P32 or P3221 along with refined model). However, Zanuda may not work well in twin case. In short, the problem now is to choose one SG from P32 or P3221. There is one suggestion that try SG P32, as there are two copies of molecules in ASU in P32 group, try find the NCS operator in P32 and check if this operator is close to crystallographic symmetry operator or not, if it is, then SG is P3221, if it's not, then SG is P32. I did a few rounds of search in Internet, I found Phenix "Find NCS tool" and input PDB of my refined structures from both P32 and P3221. For both test, Find NCS tool did find NCS operator but in the end of the log file I see the same results as below: This NCS object does not contain point group symmetry This NCS object does not contain helical symmetry. I am asking: 1. does "This NCS object does not contain point group symmetry" from Find NCS tool mean that NCS operator in my PDB is not crystallographic symmetry operator? 2. Is there a tool in Phenix which can find the NCS operator and check if the NCS operator is close to crystallographic symmetry operator or not? Thanks ahead.

2 1

Marching tomorrow?
by lbetts0508 . 22 Apr '17

22 Apr '17

Dear all, I am marching in DC tomorrow for continued support of our wonderful National Laboratories and funding that made resources like PHENIX possible. What a treasure these have been. Thank you for your support of structural biologists all these years and I hope for your continued success! Laurie Betts Chapel Hilll,NC

2 1

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.

9 9

Generate a map showing local agreement between map and model
by #AHMED TOFAYEL# 18 Apr '17

18 Apr '17

Dear developers and users, Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar figure for my project. Is it possible to do with phenix? http://emboj.embopress.org/content/28/6/755 Best regards, Tofayel NTU Singapore

4 4

UTMB Sealy Center for Structural Biology Symposium - May 6 - Register NOW
by Mark A. White 17 Apr '17

17 Apr '17

You and your colleagues are cordially invited to join us for the 22nd Annual Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island on Saturday, May 6, 2017. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: James Chou, Ph.D., Harvard Medical School Rachelle Gaudet, Ph.D., Harvard University Petr Leiman, Ph.D., Univ. of Texas Medical Branch Daniela Nicastro, Ph.D., Univ. of Texas Southwestern Medical Center Brian Shoichet, Ph.D., Univ. California San Francisco School of Pharmacy Kylie Walters, Ph.D., Center for Cancer Research, National Cancer Institute To register or for more information, visit http://scsb.utmb.edu/symposium register: http://scsb.utmb.edu/symposium/2017/registration.asp

1 0

Understanding Biology through Structure, Santa Fe May 13-17
by Terwilliger, Thomas Charles 14 Apr '17

14 Apr '17

Hi Colleagues! I hope you can come to our symposium on Understanding Biology through Structure in Santa Fe this May 13-17! The Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. You can see the full program at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Understanding Biology through Structure Santa Fe, NM May 13-17 2017 Speakers Nucleic acid and protein-nucleic acid complexes Jamie Cate, University of California, Berkeley Eva Nogales, University of California, Berkeley Jody Puglisi, Stanford University Leemor Joshua-Tor, Cold Spring Harbor Laboratory Tom Steitz, Yale University Shigeyuki Yokoyama, RIKEN Structural Biology of Cell Signaling Axel Brunger, Stanford University Sharon Campbell, University of North Carolina Yvonne Jones, Oxford University Dorothee Kern, Brandeis University Cynthia Wolberger, Johns Hopkins University Hao Wu, Harvard University Disease and Drug Discovery Lesa Beamer, University of Missouri Tom Blundell, University of Cambridge Elizabeth Goldsmith, UT Southwestern Medical Center Lynn Howell, University of Toronto Michael Rossmann, Purdue University Erica Ollmann Saphire, Scripps Institute Natalie Strynadka, University of British Columbia Ian Wilson, Scripps Institute Crystallographic Methods Wladek Minor, University of Virginia Randy Read, University of Cambridge Jane Richardson, Duke University Tom Terwilliger, Los Alamos National Laboratory Isabel Uson, Institute of Molecular Biology, Barcelona Nadia Zatsepin, University of Arizona Membrane Protein Structures Susan Buchanon, National Institutes of Health Wayne Hendrickson, Columbia University Robert Stroud, University of California, San Francisco Nieng Yan, Tsinghua University Protein folding and Design David Baker, University of Washington Ken Dill, Stony Brook University David Eisenberg, University of California, Los Angeles Susan Marqusee, University of California, Berkeley Tobin Sosnick, University of Chicago Understanding Enzyme Function Catherine Drennan, Massachusetts Institute of Technology Andrzej Joachimiak, Argonne National Laboratory Ci Ji Lim, University of Colorado, Boulder Ilme Schlichting, Max Planck Institute for Medical Research All the best, Tom T ?

1 0

Deadline approaching: 10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 13 Apr '17

13 Apr '17

Dear Colleagues, The deadline for application to the annual CCP4/APS school in macromolecular crystallography: “From data collection to structure refinement and beyond” is in less than a week - April 19. Please read the thread below for basic information on the school. For all details, please visit http://www.ccp4.ac.uk/schools/APS-2017/index.php With regards, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, February 01, 2017 2:54 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] 10th CCP4/APS Crystallographic School in the USA Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: beamline training; data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors, respectively; and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting of the technical difficulties the participants face in their projects. We have had considerable success resolving these problems in past years, attested by resulting publications http://www.ccp4.ac.uk/schools/APS-school/publications.php Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Registration fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

1 0