December 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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difference map for cryo-EM (cryo-EM map minus model map)
by Pavel Afonine 16 Mar '17

16 Mar '17

For those practicing cryo-EM and tending to use Phenix nightly builds, as well as in response to a recent post (Re: [phenixbb] difference map based on the cryo-EM map): Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps. One map is computed in real space: cryo-EM map minus model calculated map; it is locally scaled in some complex way to account for local variations and possibly poorly refined B-factors. In terms of reciprocal space it is an analog of: (F_obs, Phase_obs) - (F_calc, Phase_calc). The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved. I'm not sure which one of the two is better. Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography). Current limitations: - no GUI; - map must have origin at (0,0,0); - output file name can't be changed. To use: phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9 which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 . If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb. In future (once fully tested) this will be integrated into phenix.real_space_refine. The tool is 10 hours old and tested on just one model (5l4g, emd_4002.map), so bugs are not unexpected. Any feedback is welcome! All the best, Pavel

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Scale and merge multiple data sets
by Sam Tang 06 Feb '17

06 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

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Postdoctoral Fellow Position at US MHRP, WRAIR
by gjoyce＠hivresearch.org 30 Dec '16

30 Dec '16

Dear All, A postdoc position is available in a newly formed Structural Biology Section, part of the US Military HIV Research Program, WRAIR in Silver Spring, Maryland, USA. The position involves the application of structural biology to understanding viral glycoproteins and the immune response following vaccination or natural infection. Interested and qualified individuals can apply through the following official link at Job ID: 212324 at the Henry M Jackson Foundation careers website: http://www.hjf.org/careers/open-jobs. Applicants must be US citizens or have lived in the US for at least 3 consecutive years. Please feel free to contact me at gjoyce(a)hivresearch.org if you have any questions. Best wishes, Gordon HJF is seeking a Postdoctoral Fellow to support the Military HIV Research Program (MHRP) located at the Walter Reed Army Institute of Research (WRAIR) in Silver Spring, Maryland. The incumbent will be responsible for initiating and carrying out scientific projects, under the supervision of senior scientists and in collaboration with other research scientists. The position involves the characterization of the humoral immune response to HIV-1 infection and HIV-1 vaccines using X-ray crystallography. The incumbent will be responsible for conducting and publishing research in HIV structural biology. The incumbent will work within a multidisciplinary environment consisting of military, government, academic, and international collaborators. Responsibilities: Conducts independent research and learns techniques required to conduct the research. Assists in designing, developing, executing, and implementing scientific research and/or products. Develops a thorough understanding of the scientific literature relating to the research topics. Collects and handles samples and keeps detailed inventory and records of experiments by maintaining up to date, clear, and accurate laboratory notebooks. Executes projects related to biochemical and structural characterization of antibodies, vaccine candidates and their complexes. Analyzes experimental data, applying relevant statistical and bioinformatic models. Presents data at scientific meetings and publishes original research in peer-reviewed journals. Assists with training laboratory staff and collaborates with labs within and outside of MHRP. Follows all MHRP and WRAIR safety procedures and completes required training in a timely manner. Performs other duties as assigned. Required Knowledge, Skills, and Abilities: PhD in structural biology or related area with significant experience in X-ray protein crystallography. Knowledge of appropriate scientific area; ability to analyze and interpret data. Experience and proficiency in protein purification, protein characterization, X-ray crystallography including up-to-date knowledge of relevant programs including CCP4, and Phenix packages. Experience with project planning, implementation, and data analysis. Experience in presenting at scientific meetings and writing manuscripts for scientific journals. Practical knowledge of electron microscopy, molecular modelling or structure-based mutagenesis and design is an advantage. Minimum Education/Training Requirements: Ph.D. in structural biology, molecular biology, immunology, microbiology, biochemistry or related discipline. Minimum Experience: 0-2 years of postdoctoral experience Physical Capabilities: Long periods of standing and sitting; intricate work with hands; carrying of light and moderately heavy laboratory equipment. Job performance requires movement around and between several laboratories, and long periods of sitting at laboratory bench. Fine motor coordination in manipulation of laboratory materials is essential. Supervisory Responsibilities/Controls: May provide guidance to laboratory staff. Work Environment: Laboratory environment; may require working evenings and weekends. The incumbent will be expected to practice safe handling of hazardous chemicals. This laboratory is densely populated and requires good interpersonal skills for effective job performance. This position requires working and occasional travel to US synchrotron facilities. This Postdoctoral Fellow will support the US Military HIV Research Program, located at The Walter Reed Army Institute of Research (WRAIR) in Silver Spring, MD. HJF is an equal opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, or protected veteran status. Any qualifications to be considered as equivalents, in lieu of stated minimums, require the prior approval of the Director of Human Resources. M. Gordon Joyce, Ph.D. Chief, Structural Biology Section The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 gjoyce(a)hivresearch.org Web: www.hivresearch.org Facebook: www.facebook.com/hivresearch YouTube: www.youtube.com/mhrpvideos Twitter: www.twitter.com/mhrpinfo The U.S. Military HIV Research Program (MHRP), centered at the Walter Reed Army Institute of Research (WRAIR), is an international HIV vaccine research program that successfully integrates HIV/AIDS prevention, care and treatment.

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Spring 2016 MicroED workshops at Janelia Research Campus
by Hattne, Johan 23 Dec '16

23 Dec '16

Due to high demand, two back-to-back MicroED workshops will be held at Janelia Research Campus (Ashburn, VA) in the spring. The workshops are hosted by Tamir Gonen and will have the same content. Accepted participants will be assigned by the organizers to one or the other (not both). May 21-24 and May 24-27, 2017 MicroED is a cryoEM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryoTEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To facilitate the widespread use of MicroED, we are offering these workshops to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Applicants must register and submit a brief statement on why they wish to participate, via our online registration system. https://conference.janelia.org Please note that this system is designed to collect abstract information for presentations. Please write your statement of interest in the "abstract" field, put your name in the "author" field, and put "n/a" in the "presentation title" and "keyword" fields. Space in these workshops is limited. The application deadline is February 10, 2017. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

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Job opportunity - Structural Biology GSK Vaccines
by Enrico Malito 22 Dec '16

22 Dec '16

Dear phenix community, The Structural Biology Lab at GSK Vaccines, Rockville, MD, USA, is seeking a candidate for a Scientist/Senior Scientist position (Job ID: 148543, hiring managers: Enrico Malito, Matthew Bottomley). We offer outstanding opportunities and compensation to outstanding candidates. Anyone interested to apply can do so by visiting this link: https://careers.peopleclick. com/careerscp/client_gsk/external1931/en-us/gateway.do? functionName=viewFromLink&jobPostId=323652&localeCode=en-us (Please note that this may wrap to another line of text; you may need to copy and paste the entire URL into your browser window). Applications will be accepted only through the page at the link above. Examples of relevant recent publications: - Rappuoli et al 2016. Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design. http://dx.doi.org/10.1084/jem.20151960 - Chandramouli et al 2015. Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody http://dx.doi.org/10.1038/ncomms9176 - Ciferri et al 2015. Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies http://dx.doi.org/10.1371/journal.ppat.1005230 - Malito et al 2015. Protein Crystallography in Vaccine Research and Development. http://dx.doi.org/10.3390/ijms160613106 Yours sincerely, *Enrico Malito, PhD* *Lab Head of Structural Biology and BiophysicsGSK VaccinesPreclinical R&D USGSK Vaccines14200 Shady Grove Road, Rockville MD 20850, USA*

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alingments in mr_rosetta
by Kajander, Tommi A 21 Dec '16

21 Dec '16

Hi, I am wondering about the alignment of sequence and PDB model in mr_rosetta - the program seems to complain if the sequences dont exactyl match - so is this really the case? (I have an initial model from autobuild with some fragments that do not have fully correct sequence - hence it doenst exactly match with the original sequence of the protein). Does it have to? Or should there be a way around it? also the command file examples online e.g. : phenix.mr_rosetta \ seq_file=seq.dat \ data=coords1.mtz \ search_models=coords1.pdb \ already_placed=True \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies=2 \ space_group=p212121 \ use_all_plausible_sg=False \ nproc=200 \ group_run_command=qsub when using the command file all the commands are not recognized for some reason (running on a mac with bash shell) e.g. rescore_mr.relax=False, same with fragment files… not quite sure what the problems is there, probably something trivial. -if i just enter them on the command line it works. Thanks, Tommi

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Error from f_model_all_scales.py
by John Bruning 20 Dec '16

20 Dec '16

Hi (Pavel), I have a dataset (P31) which I am processing with the pairwise combinations of reindexing operators (4 incl. no reindexing therefore h,k,l) and twin laws (4 incl. no twinning as h,k,l). While some of these combinations are fine during refinement (Vers 1.11.1), for some combinations I get the following error, which ultimately kills the refinement. Thanks in advance and apologies if I am missing something stupid. Incidentally, a different dataset seems to tolerate all combinations. *approx_equal eps: 1e-05* *approx_equal multiplier: 10000000000.0* *0.512707954357 approx_equal ERROR* *0.514972857238 approx_equal ERROR* Traceback (most recent call last): File "/Applications/phenix-1.11.1-2575/build/../modules/phenix/ phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/command_line.py", line 154, in run call_back_handler=call_back_handler) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/driver.py", line 1529, in run call_back_handler = call_back_handler).result File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/strategies.py", line 121, in __init__ log = log) File "/Applications/phenix-1.11.1-2575/modules/phenix/phenix/refinement/fmodels.py", line 159, in run fmodel.update_solvent_and_scale(initialise=True) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/twinning/twin_f_model.py", line 797, in update_solvent_and_scale params=params, log=log, apply_back_trace=apply_back_trace) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1457, in update_all_scales params = params, log = log, refine_hd_scattering=refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 38, in __init__ refine_hd_scattering = refine_hd_scattering, log = log) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 61, in compute refine_hd_scattering = refine_hd_scattering) File "/Applications/phenix-1.11.1-2575/modules/cctbx_project/ mmtbx/bulk_solvent/f_model_all_scales.py", line 329, in update_solvent_and_scale_twin * assert approx_equal(self.r_all(), o_kbu_sol.r(), 1.e-5)* *AssertionError*

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phenix rosetta interface
by CPMAS Chen 17 Dec '16

17 Dec '16

Hi, All, When I compile phenix-1.11-2567 and rosetta-bin-mac_2016.37.58930_bundle interface, I got the following error message. Any suggestion to fix this? Thanks! src/core/scoring/cryst/PhenixInterface.cc:253:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( pdbout , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ src/core/scoring/cryst/PhenixInterface.cc:916:11: error: no matching member function for call to 'dump_pdb' pose_asu.dump_pdb( buffer , "1" ); ~~~~~~~~~^~~~~~~~ src/core/pose/Pose.hh:1525:2: note: candidate function not viable: no known conversion from 'char [256]' to 'std::ostream &' (aka 'basic_ostream<char> &') for 1st argument dump_pdb( ^ src/core/pose/Pose.hh:1518:2: note: candidate function not viable: requires single argument 'file_name', but 2 arguments were provided dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate function not viable: requires single argument 'out', but 2 arguments were provided dump_pdb(std::ostream & out) const; ^ 2 errors generated. scons: *** [build/src/release/macos/16.1/64/x86/clang/8.0/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. Thanks! -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Asymmetric unit content
by Sharan Karade 13 Dec '16

13 Dec '16

Dear all, I have solved the structure in C121 space group, having five molecules in asymmetric unit, my supervisor have doubt about the fifth molecule becoz of poor density fit, if i delete the fifth molecule, there is a space for the molecule and crystal is not continuous, i calculated difference map from Phenix by deleting fifth molecule and got the Map showing presence of molecule. My supervisor want me to get SetMet data, but crystals are diffracting poor (7A). Is there any way to convince my guide. advance thanks for valuable suggestions. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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