October 2016 - phenixbb - phenix-online.org

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

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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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Failed to refine B factors of some residues and ligands
by Zhou, Tongqing (NIH/VRC) [E] 16 Nov '16

16 Nov '16

Dear All, I am refining a structure with diffraction to 2.2A resolution and 95 % overall completeness. Now the Rs are at 18% and 23%, respectively. But the program failed to refine B factors for several ligands, atoms had high B factors while showing positive Fo-Fc map around them. Occupancy was set to 1 and I also tried to reset B to mean B of the whole PDB. Any of you seeing this phenomenon? Thanks! Shown below is HEPES that has high B factor and positive density around it after refinement: [cid:[email protected]] Best regards, Tongqing Tongqing Zhou, Ph.D. Co-head and Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4609B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 761-7068 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

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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 28 Oct '16

28 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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