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phenix gui starting up for one, not for other users
by wtempel 01 Nov '16

01 Nov '16

Hello, we run phenix on a ubuntu 14.04 (x86_64) box. Phenix is installed in user x’s home directory. After running . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, and some *setlocale* warnings, the phenix GUI will show up on the screen for user x. User y, after . ~x/prog/phenix-1.11.1-2575/phenix_env.sh; phenix, will get *setlocale* warnings, a white credit screen (briefly), but the GUI will not show up, but *phenix* does not exit. User does get the expected error messages after typing phenix.molprobity_1.11.1-2575 without specifying input coordinates, as does user y get the (older) GUI upon . ~x/prog/phenix-1.10.1-2155/phenix_env.sh; phenix. Do you have any suggestions as to how I can enable user y to use the 1.11.1 GUI? Thank you. Wolfram Tempel

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postdoc jobs at Oxford
by Cell Guidance 01 Nov '16

01 Nov '16

Hello, May I please draw your attention to two excellent postdoc opportunities at the University of Oxford. Further information is available via the links below. Application deadlines are 30 November and 1 December 2016. Postdoc in Structural Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Postdoc in Cell Biology: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Many thanks, Elena Dr. Elena Seiradake Dept. of Biochemistry, University of Oxford South Parks Road, Oxford, OX1 3QU, U.K.

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Viewing different residues in the same location in Coot.
by Nigel Moriarty 28 Oct '16

28 Oct '16

Folks Phenix has the ability to refine two different amino acids (using alt. loc.) in the one place like in 1ejg. You can read more about it here. https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 This crashes Coot until you add allow_duplicate_sequence_numbers() to $HOME/.coot.py in OSX or the appropriate place on Windows. For Windows, as there is no $HOME, Coot uses .coot.py or .coot-preferences/ directory for configuration - these can be found (added to) the directory in which Coot was installed (e.g. C:\WinCoot). Nigel PS While you're at it, why not add these lines below to automatically load FEM and polder maps. set_auto_read_column_labels("FEM", "PHIFEM", 0) set_auto_read_column_labels("mFo-DFc_polder", "PHImFo-DFc_polder", 1) --- 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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rosetta.build_phenix_interface errors
by Gerhard Fischer 28 Oct '16

28 Oct '16

I am having some trouble setting up phenix.rosetta_refine on my Kubuntu 16.04 LTS-system. I've been following the instructions found here: https://www.phenix-online.org/documentation/reference/rosetta_install.html The installation/compilation of Rosetta as such (rosetta_src_2016.37.58930_bundle.tgz) worked fine, and so did installing the latest version of Phenix - here, I've tried both the binary available for download (phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6) and a self-compiled version (phenix-installer-1.11-2567-source). But when running rosetta.build_phenix_interface (both with nproc=6 or no multiple processor options set), the compilation crashes at some point. This takes quite a while, and I suspect most parts get compiled, but it does not run to completion. Any ideas? I attach the output of the error message below. Best wishes, Gerhard ------ stdout ---- g++ -o build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os -c -std=c++11 -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_STD -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/5.4 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal/libxml2/include -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:253:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( pdbout , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:916:34: error: no matching function for call to 'core::pose::Pose::dump_pdb(char [256], const char [2])' pose_asu.dump_pdb( buffer , "1" ); ^ In file included from src/core/scoring/cryst/PhenixInterface.cc:18:0: src/core/pose/Pose.hh:1518:2: note: candidate: bool core::pose::Pose::dump_pdb(const string&) const dump_pdb(std::string const & file_name) const; ^ src/core/pose/Pose.hh:1518:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1521:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&) const dump_pdb(std::ostream & out) const; ^ src/core/pose/Pose.hh:1521:2: note: candidate expects 1 argument, 2 provided src/core/pose/Pose.hh:1525:2: note: candidate: void core::pose::Pose::dump_pdb(std::ostream&, const utility::vector1<long unsigned int>&) const dump_pdb( ^ src/core/pose/Pose.hh:1525:2: note: no known conversion for argument 1 from 'char [256]' to 'std::ostream& {aka std::basic_ostream<char>&}' src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::fitBfactors(core::pose::Pose&)': src/core/scoring/cryst/PhenixInterface.cc:244:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:375:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'void core::scoring::cryst::PhenixInterface::initialize_target_evaluator(const core::pose::Pose&, std::__cxx11::string)': src/core/scoring/cryst/PhenixInterface.cc:914:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1080:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ src/core/scoring/cryst/PhenixInterface.cc: In member function 'std::__cxx11::string core::scoring::cryst::PhenixInterface::calculateDensityMap(core::pose::Pose&, bool)': src/core/scoring/cryst/PhenixInterface.cc:1100:25: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(tempdir_.c_str()); ^ src/core/scoring/cryst/PhenixInterface.cc:1109:13: warning: ignoring return value of 'int chdir(const char*)', declared with attribute warn_unused_result [-Wunused-result] chdir(".."); ^ scons: *** [build/src/release/linux/4.4/64/x86/gcc/5.4/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: building terminated because of errors. --------- stdout end ------ -- Gerhard Fischer, PhD Postdoctoral Research Associate University of Cambridge Department of Biochemistry 80 Tennis Court Road CB2 1GA Cambridge United Kingdom --- This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Fix coordinates of one single residue
by ancacarl 28 Oct '16

28 Oct '16

Hi, I'm working on the refinement of a protein mutated with an unnatural amino acid that is present as two rotamers. Whenever I do refinements, one of the rotamers moves away from the electron density map. I therefore would like to fix the coordinates for this amino acid only while continuing the refinement of the rest of the protein. Is there a way in Phenix to do this? Any advice is welcome. Best regards, Anna-Carin

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Fwd: Re: AW: phenix.real_space_refine
by Pavel Afonine 27 Oct '16

27 Oct '16

Hi Julia, > but I need to try different weightings to find the optimal one, so > this is not an option. no need to try different weights - the program does this for you automatically. If it doesn't - please report a bug. All the best, Pavel

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GUP deadline approaching for APS Beamtime at NE-CAT
by Salbego, Cyndi 27 Oct '16

27 Oct '16

NE-CAT is accepting GUP proposals for the 2017-1 run cycle. Please choose 24-ID-C or 24-ID-E as your first choice to be scheduled with NE-CAT! The 24-ID-C beamline can deliver X-rays in the range of 6 to 21 keV or ~2.1 to 0.5 Å. This covers most of the popular elemental edges for phasing. This wide energy-range also makes the beamline well suited for ultra high-resolution data collection and soft X-ray sulfur SAD phasing. The beamline is equipped with an optional kappa goniometer for optimal alignment of crystals. A Pixel Array Detector (PAD), Pilatus-6MF, installed on the 24-ID-C beamline helps measure very weak Bragg reflection intensities due to its noise-less readout technology and also provides a very fast data collection capability in shutter-less data collection mode. The 24-ID-E beamline is a fixed energy microdiffraction beamline delivering X-rays at 12.66 keV, optimized for Se-SAD experiments. It is equipped with a CCD-based ADSC Quantum 315 detector. Both beamlines are equipped with state-of-the-art instrumentation to handle advanced data collection methods. MD2 microdiffractometers installed at both beamlines provide very clean beams from 5 microns to 100 microns in diameter and have exceptional sample visualization systems capable of visualizing micron-sized crystals with extreme clarity. Deadline Friday, October 28, 2016 for: - New General User Proposals (GUPs) - New Beam Time Requests for APS run 2017-1 (1/31/2017 - 4/24/2017) on existing active proposals - Partner user proposals (PUPs) - CAT Member Proposals - APS Beamline Staff Proposals - CAT Beamline Staff Proposals The GUP system (https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page) will accept proposals and beam time requests until 11:59 pm (Chicago time) on October 28, 2016. However, User Office support will not be available after 5:00 pm that day. If you feel you may need help during the submission process, please create your proposal as early as possible. For questions about the GUP system or the proposal submission process, please contact gu_program(a)aps.anl.gov<mailto:[email protected]>. For guidance on the Proposal System, see https://www1.aps.anl.gov/Users-Information/About-Proposals/Concepts-Definit…. For general inquiries, please feel free to contact the User Office (630-252-9090, apsuser(a)aps.anl.gov<mailto:[email protected]>) Cyndi Salbego Administrator, NE-CAT 630.252.0689

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tNCS
by Huyton, Trevor 25 Oct '16

25 Oct '16

Dear All, I have been struggling for while with a Molecular replacement problem for a large complex(3 proteins) with 2 copies per ASU. I have a small but 100% model for one of the components but this contributes only 12% of ASU (2 molecules) a much poorer <20% model that contributes the majority 80% of the ASU Space group is P222>P212121 best MR is in P21221. I have strong tNCS as seen in native patterson and phaser chooses this top peak in MR runs: There was 1 non-origin distinct peak (i.e. over 20% of origin peak and more than 15 angstroms from the origin) Sorted by Height ---------------- Height Distance Vector 56.0% 126.4 : FRAC +0.5000 +0.5000 +0.3500 (ORTH 63.0 88.0 65.4) Molrep also uses the same tNCS vector: --- Check Patterson for pseudo-translation --- PST_limit : 0.125 of origin peak INFO: pseudo-translation was detected. Origin Patterson peak: P,P/sig : 26479.002 239.412 1 Patterson peak : p,P/sig : 13591.399 122.888 2 Patterson peak : P,P/sig : 2506.590 22.664 3 Patterson peak : P,P/sig : 1517.345 13.719 Peak 1: trans.vector /ort/ : 62.995 88.023 65.691 trans.vector /frac/: 0.500 0.500 0.352 Peak 2: trans.vector /ort/ : 0.000 0.000 55.510 trans.vector /frac/: 0.000 0.000 0.297 Peak 3: trans.vector /ort/ : 58.238 88.023 65.730 trans.vector /frac/: 0.462 0.500 0.352 INFO: translation vector of peak 1 will be used. My question is how does this affect my MR with the smaller component? Is it exactly the same vector as the larger component? Thanks Trevor

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Re: [phenixbb] phenix.real_space_refine
by Pavel Afonine 24 Oct '16

24 Oct '16

On 10/24/16 23:50, Pavel Afonine wrote: > I think "weight=1" may be a troublemaker.. It may be too far from > what's optimal (that program determines by default if you don't > specify any weight) and that may result in clashes that happen during > refinement. Of course, something else may cause this as well. > > Pavel > > On 10/24/16 20:07, Oleg Sobolev wrote: >> Hi Julia, >> >> In addition to Dorothee's response to your another e-mail, I would >> indeed recommend check the model geometry, in particular, bad atomic >> clashes (where 2 atoms are very close to each other). You can find >> them in the .geo file which should be created by this point or in >> log, under "Nonbonded interactions:". The worst clashes will be the >> first in the list. >> >> Best regards, >> Oleg Sobolev. >> >> On Mon, Oct 24, 2016 at 3:19 AM, Flis, Julia <julia.flis(a)charite.de >> <mailto:[email protected]>> wrote: >> >> Hello, >> >> my question is about the Phenix real space refinement. I am using >> the Phenix version phenix-1.11-2563. >> >> My command looks as follows: >> phenix.real_space_refine secondary_structure.enable=true >> Model.pdb VOL.map elbow.Model_pdb.001.cif Model.pdb_ss.eff >> resolution=3.8 weight=1 >> >> My problem is that the refinement suddenly stops during the first >> refinement cycle: >> >> >> >> Model_real_space_refined.log says: >> >> ********************** REFINEMENT MACRO_CYCLE 1 OF 5 >> ************************* >> ------------------------------------------------------------------------------- >> Update NCS operators >> ******************** >> ------------------------------------------------------------------------------- >> Update rotamer restraints >> ************************* >> ------------------------------------------------------------------------------- >> Global refinement >> ***************** >> END >> >> >> In the shell I get this : >> >> [...] >> distance: 184426 - 184921: 3.388 >> distance: 184428 - 184920: 3.342 >> distance: 184448 - 184898: 3.373 >> distance: 184449 - 184897: 3.187 >> distance: 184491 - 184860: 3.066 >> distance: 184531 - 184770: 3.203 >> distance: 184554 - 184746: 3.137 >> >> then it stops and the only files generated are >> Model_real_space_refined.log and Model_initial.geo. >> >> Could you give me an advise? I have no clue what the problem >> could be. >> >> Thank you, >> >> Julia >> >> >

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Post for Ass. Prof. position
by Nigel Moriarty 24 Oct '16

24 Oct '16

Dear Phenix community, An *Assistant Professor position in microbiology or biochemistry* (Position # 22809) is currently open in the Department of Microbiology, University of Manitoba, Canada. Structural biology (protein X-ray crystallography) is a key strength of our Department and so applicants with such a background are encouraged to apply. Please see the ad below for details. *For further information contact the Search Committee Chair <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>>. The closing date for receipt of applications is Friday, January 6, 2017* ——— The Department of Microbiology invites applications for a full-time tenure-track position at the Assistant Professor level, commencing July 1, 2017, or on a date hing and research. Outstanding candidates in any area of Microbiology or Biochemistry will be considered, with particular emphasis on candidates who will complement or extend the department’s strengths. The successful candidate will have a Ph.D. and preferably post-doctoral experience or industry experience or other distinguishing attributes in host-microbe interactions, antibiotic resistance and drug discovery, structural biology, protein and membrane biochemistry, systems microbiology, and industrial and applied microbiology, or a related field. Duties will involve research, including the establishment of an externally funded research program, undergraduate teaching, graduate teaching and supervision, and service-related activities. The successful candidate will have a track record of high quality scholarly research leading to peer assessed publications; will either have, or demonstrate the potential to establish, an independent, innovative, scholarly, externally fundable research program; will have demonstrated strength in or strong potential for outstanding teaching contributions; and will exhibit evidence of the ability to work in a collaborative environment. Salary will be commensurate with experience and qualifications. To enhance our department and create role models for a diverse population of students, we particularly invite application from those who can support and enhance our diversity, including women, Indigenous peoples, other visible minorities, and those committed to a diverse environment. The Department currently has twelve full time tenured and tenure track faculty members and three Instructors, and offers a full range of both undergraduate and graduate programs in Microbiology and Biochemistry. The Department has a well-established and equipped research facility, including X-ray crystallography and large scale mammalian and prokaryotic cell culture facilities, as well as access to state of the art light microscopy, electron microscopy, and small angle x‑ray scattering instrumentation, and is supported by strong research links with other University of Manitoba departments including Chemistry, Biological Sciences, Physics, Biosystems Engineering, Biochemistry and Medical Genetics, and Plant Science and with the National Microbiology Laboratory of the Public Health Agency of Canada in Winnipeg. Further information about the Department can be obtained from <www.sci.umanitoba.ca/microbiology>. Winnipeg is the largest city in the Province of Manitoba. The city has a rich cultural environment, including symphony, opera, dance, theatre, and ethnic festivals and professional hockey and football. The region provides ample opportunities for outdoor recreation in all seasons. Learn more about Winnipeg at <winnipeg.ca>. The University of Manitoba is strongly committed to equity and diversity within its community and especially welcomes applications from women, members of racialized communities, Indigenous persons, persons with disabilities, persons of all sexual orientations and genders, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. *Applications including a curriculum vitae, a description of teaching philosophy, a summary of research interests, a three page research plan and contact information for three references should be sent to <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>> (a single PDF file is preferred). Please ensure to specify position number 22809 in the application. For further information contact the Search Committee Chair at <Deborah.Court(a)umanitoba.ca <Deborah.Court(a)umanitoba.ca>>. The closing date for receipt of applications is Friday, January 6, 2017.* Application materials, including letters of reference, will be handled in accordance with the Freedom of Information and Protection of Privacy Act. Please note that curricula vitae may be provided to participating members of the search process. -------- Brian ============================== Brian Mark, MSc, PhD Associate Professor Department of Microbiology & Department of Biochemistry and Medical Genetics Mailing/Courier address: Department of Microbiology Rm 213 Buller Building University of Manitoba 45 Chancellor's Circle Winnipeg, Manitoba CANADA R3T 2N2 Phone (204) 480-1430 Fax (204) 474-7603 Web: http://home.cc.umanitoba.ca/~bmark/Welcome.html 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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