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

4 5

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

6 15

Failed to refine B factors of some residues and ligands
by Zhou, Tongqing (NIH/VRC) [E] 15 Nov '16

15 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. ******************************************************************

4 8

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

1 0

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

1 0

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

1 0

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 >> >> >

1 0

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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Re: [phenixbb] XN-refinement
by Pavel Afonine 17 Oct '16

17 Oct '16

>> this is good to hear, and this demonstrates the power of using more data. The only issue here, as I mentioned before, is that in joint XN refinement we refine one single model against two data sets, while ideally it should be two models in order to account for genuine unique information that is contained in X-ray and neutron data. This will be addressed at some point. >> > Out of curiosity, could you elaborate on why it would be preferred to refine two separate models? It seems to me, admittedly not having any experience with neutron diffraction, that the ultimate goal is to model the system of the crystal, and given 2 data sets, we would want to create the single model describing the structure in the crystal that best agrees with all the available data. Are the neutron and X-ray data so different that using them for joint refinement is disadvantageous? I think I wrote that already in previous email.. Structures corresponding to two data sets are of course overall similar may be different in local details: - Different X-H(D) distances (see figure 4 here: http://journals.iucr.org/d/issues/2010/11/00/dz5209/index.html) - Different data collection temperatures: -- Different B factors; -- Different visible water structure; -- Different local disorder (that may be captured as distinct conformations at low temperature, but may be blurred at higher temperature); - Different completeness and resolution of one data set may allow features in one model corresponding to this data set that may not be supported by the other data set. For example, you may see a well resolved water with one or two D in neutron map but you may not even see any water at all in X-ray map, or the other way around. - etc etc etc. So it is advantageous to use both X-ray and neutron data sets together but these nuances need to be carefully taken care of which isn't the case in current implementations of joint XN refinement protocols. This makes a good room for future improvements. Pavel

3 2

constrain insertion codes to unit occupancy?
by van den Bedem, Henry 15 Oct '16

15 Oct '16

Hi: I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this ATOM 6500 CA ACYS B 101B ATOM 6490 CA BXXX B 101A How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb. Thanks! Henry

4 4

XN-refinement
by Johannes Schiebel 14 Oct '16

14 Oct '16

Hi everyone, I am currently working on an X-ray/neutron (XN) joint refinement using phenix.refine. As it should be, H/D coordinates and ADPs at exchangable sites are refined to equal values when using Phenix version 1.10.1-2155 and neutron data only. This is also stated in the paper describing the development of the method (Afonine et al. (2010) Joint X-ray and neutron refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 66, 1153-1163) as the default behavior: "Currently, phenix.refine maintains the H and D atoms at coinciding positions and constrains their ADPs to be equal to each other". However, when switching to XN-refinement using the same Phenix version, H and D atoms refine to different coordinates and ADPs, which should not be the case as it leads to unrealistic artifacts as can be seen from the deposited PDB 3X2P: ATOM 186 H AALA A 13 3.486 -18.200 -14.123 0.38 14.54 H ATOM 187 D BALA A 13 3.488 -18.195 -14.111 0.62 38.07 D In this example, the D-occupancy is likely overestimated, while the H-occupancy is underestimated because the ADPs refine to very different values, which is chemically not reasonable. Hence my question: How can I treat my data in a way that ADPs and coordinates refine to the same values at exchangeable H/D sites also for XN-refinement? Is there a specific keyword I am currently overlooking or do I have to use another Phenix version? I would be really glad to receive your feedback. Thanks in advance! Kind regards, Johannes

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Unknown parameter file format
by Jan van Agthoven 11 Oct '16

11 Oct '16

Hi everyone, I used my refinement parameters in the following format in the latest phenix: custom_par.params And it returned: Sorry: Unknown file format: custom_par.params Anyone knows how to solve this? Thanks, Jan

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Re: [phenixbb] Highly anisotropic data
by Pavel Afonine 07 Oct '16

07 Oct '16

Hi Kostya, phenix.resolution reports effective resolution of data set. It is based on methods described here: J. Appl. Cryst. (2015). 48, 589-597 Acta Cryst. (2013). D69, 1921-1934 As I pointed out before, a single number for highest resolution isn't very informative unless you show data completeness per resolution (in phenix.refine log file it is reported in the beginning of macro-cycles right after bulk-solvent step). Pavel On 10/7/16 00:15, Kogan, Konstantin wrote: > Dear all, > > Thank you for your comments. The maps are not that bad, and actually > from biological point of view we do see everything we want. One of the > questions is how to report the parameters for the structure, as I have > a feeling that the effective resolution is much lower than 2.64Å, > which is the current limit, and the mean B value is twice higher than > estimated Wilson B value. All together it seems that this is the data > I have, but I would like to be sure, that I have got maximum out of it. > > I attach the xtriage log file for more information, if needed. Also I > attached the example of a good map region at 1.6 sigma and a bad map > region at 1.0 sigma. > > I have also tested to refine at 2.8, 2.9, and 3.0, and I haven't seen > much difference in maps quality, but the Rwork/Rfree went down a bit. > > Isn't is seems a bit suspicious 2.64Å resolution, > Rwork/Rfree=0.28/0.31, and mean B value 114? Is there a way to > present/report effective resolution? > > Kostya > > > > > Hi Kostya, > > how complete the data set is? Missing reflections in some resolution > zones between 2.64A and inf may be sufficient to make the effective > resolution lower or much lower than 2.64A which would explain why the > map does not look like what you expect. > > Pavel > > > On 05/10/16 22:53, Randy Read wrote: >> Hi, >> >> As Christian said, the level of anisotropy is not that bad for this >> structure. In terms of what Phenix can do to handle it, first, when >> you solved it by MR, Phaser would have accounted explicitly for the >> anisotropy. In fact, Phaser’s algorithms underlie the anisotropy >> server that produced your plot! Phenix.refine will also refine the >> overall anisotropy parameters. >> >> When you have really severe anisotropy, the current algorithms may >> not account well enough for the differing accuracy of reflections in >> the weak directions. So it can sometimes be helpful to do >> anisotropic pruning of the data in the way that the anisotropy server >> implements it. But this is something to do with some caution, and I >> think you should only press on with it if the maps allow you to see >> things you couldn’t see clearly before. >> >> Best wishes, >> >> Randy Read >> >> ----- >> Randy J. Read >> Department of Haematology, University of Cambridge >> Cambridge Institute for Medical Research Tel: +44 1223 336500 >> Wellcome Trust/MRC Building Fax: +44 1223 336827 >> Hills Road E-mail: rjr27(a)cam.ac.uk >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> >>> On 5 Oct 2016, at 20:32, Christian Roth <christianroth034(a)gmail.com> >>> wrote: >>> >>> Hi Kostya, >>> >>> I have seen worse data than that, which are ususally treated quite >>> well within phenix using standard parameters. With a resolution of >>> about 2.7 Ang. I wouldn't expect to see waters and also just well >>> ordered side chains, whereas more flexible ones just give some >>> "bumps" pointing away from the main chain density. Though without a >>> picture or something else it is difficult to say if your maps are >>> really unusually bad. >>> >>> Cheers >>> >>> Christian >>> >>> Am 05.10.2016 um 07:47 schrieb Kogan, Konstantin: >>>> Dear all, >>>> >>>> I have highly anisotropic data. I was able to solve the structure >>>> by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 >>>> with Resolution cutoff 2.64Å and mean B values 114, which is pretty >>>> high for such resolution. Though the overall structure makes sense, >>>> the maps are quite featureless, no water molecules, and side-chains >>>> refinement is a problem. I have tested how the data is anisotropic >>>> with Diffraction Anisotropy Server (see attached image), which >>>> shows clearly, that we don't really have data to 2.64Å in all >>>> directions. Though, there are other servers/programs that can deal >>>> specifically with anisotropic data e.g. STARANISO anisotropy server >>>> and then refine with BUSTER, I would like to know if it's possible >>>> still to use Phenix with some more advance parameters to actually >>>> address the issue of anisotropy and to get maximum out of the data. >>>> The space group is P61 2 2, cell parameters are 73, 73, 453, 90, >>>> 90, 120 and I have high multiplicity data, but no NCS. >>>> >>>> Thanks in advance for any input, >>>> >>>> Kostya >>>> -- >>>> Konstantin (Kostya) Kogan >>>> Postdoctoral researcher >>>> Pekka Lappalainen's Lab >>>> Institute of Biotechnology >>>> University of Helsinki >>>> Helsinki, Finland >>>> Mobile: +358-(0)45-8994342 >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> Unsubscribe: >>>> phenixbb-leave(a)phenix-online.org >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org

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Option to select array from mtz in phenix.real_space_refine?
by Oliver Clarke 06 Oct '16

06 Oct '16

Hi, I find phenix.real_space refine very effective for initial refinement of a model against a density modified map after molecular replacement (with morphing and reference restraints etc enabled). However, when I do this it seems like if there is more than one array of map coefficients in the file there is no way to select which columns to use, unlike for phenix.refine - would it be possible to add such an option? Currently I just use cad in ccp4 to make a file with the desired columns, but it would be a smoother process if the desired column labels could be specified directly at run time. Cheers Oli

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Highly anisotropic data
by Kogan, Konstantin 06 Oct '16

06 Oct '16

Dear all, I have highly anisotropic data. I was able to solve the structure by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 with Resolution cutoff 2.64Å and mean B values 114, which is pretty high for such resolution. Though the overall structure makes sense, the maps are quite featureless, no water molecules, and side-chains refinement is a problem. I have tested how the data is anisotropic with Diffraction Anisotropy Server <https://services.mbi.ucla.edu/anisoscale/> (see attached image), which shows clearly, that we don't really have data to 2.64Å in all directions. Though, there are other servers/programs that can deal specifically with anisotropic data e.g. STARANISO anisotropy server <http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi> and then refine with BUSTER, I would like to know if it's possible still to use Phenix with some more advance parameters to actually address the issue of anisotropy and to get maximum out of the data. The space group is P61 2 2, cell parameters are 73, 73, 453, 90, 90, 120 and I have high multiplicity data, but no NCS. Thanks in advance for any input, Kostya -- Konstantin (Kostya) Kogan Postdoctoral researcher Pekka Lappalainen's Lab Institute of Biotechnology University of Helsinki Helsinki, Finland Mobile: +358-(0)45-8994342

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