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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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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

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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

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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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