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Phenix.model_vs_data - Rfree difference
by Luca Pellegrini 02 Jan '17

02 Jan '17

Hello, I am trying to find out the reason for a large R-free difference that I am getting between phenix.refine and phenix.model_vs_data: phenix.refine R-work/R-free 0.1702/0.1974 phenix.model_vs_data R-work/R-free 0.1728/0.1795 Initial refinement was using the intensities in an XDS_ASCII.HKL dataset, followed by a few refinement cycles against the same dataset, but using amplitudes calculated in Aimless, with the ‘skip scaling just merge’ option and keeping the FreeR reflections. When I checked R-free values for the last refinement run before the conversion, there was no large discrepancy: phenix.refine R-work/R-free 0.1720/0.2086 phenix.model_vs_data R-work/R-free 0.1715/0.2080 Can anyone please advise? Apart from this, refinement went well - both the 1.9A map and the model look fine. Thanks for the help & happy New Year, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA UK Email: lp212(a)cam.ac.uk Phone: 0044-1223-760469

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Postdoctoral Fellow Position at US MHRP, WRAIR
by gjoyce＠hivresearch.org 29 Dec '16

29 Dec '16

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

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Spring 2016 MicroED workshops at Janelia Research Campus
by Hattne, Johan 22 Dec '16

22 Dec '16

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

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

22 Dec '16

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

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

21 Dec '16

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

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Error from f_model_all_scales.py
by John Bruning 19 Dec '16

19 Dec '16

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

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phenix rosetta interface
by CPMAS Chen 16 Dec '16

16 Dec '16

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

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Asymmetric unit content
by Sharan Karade 12 Dec '16

12 Dec '16

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

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Recent improvements in Phaser for systematically weak data
by Randy Read 09 Dec '16

09 Dec '16

Dear all, Between the last official release of Phenix (version 1.11.1-2575, released on 26 October) and a recent CCP4 update (7.0.023 released on 23 November), we fixed a problem in which the fast rotation function was not properly accounting for the effect of measurement errors in intensities. Under many circumstances (i.e. with well-measured data to the resolution needed to solve the structure by MR), the change is not noticeable. However, if you have systematically weak data (particularly from high levels of anisotropy or potentially from the effects of translational non-crystallographic symmetry), the fix can mean the difference between failing to solve the structure, because the correct orientation has not been generated, or solving it with a default run of Phaser. We recommend that anyone trying to solve a structure with substantial anisotropy (anisotropic deltaB of 50 A^2 or greater) and/or translational NCS should update to a newer version of either package. If you're using CCP4, you should get the latest update, because there was a problem with the version of coot distributed with the 7.0.023 update. If you're using Phenix, you should get a recent nightly build, i.e. dev-2608 or something even newer. Please note that you want to provide data to Phaser in the form of intensities rather than amplitudes to get the best results for such data! So far, I've found 3 of our test cases where this makes a real difference, but I would be interested in hearing from anyone who finds that this makes a difference for other cases. 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

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iNEXT access: NMR Extended Support and more!
by Anastassis Perrakis 06 Dec '16

06 Dec '16

Dear all, I should perhaps offer sincere apologies for posting the crystallography boards with NMR news ;-). However, I will not do that, as I sincerely hope you will see that in an era of integration of structural methods, such opportunities can offer the chance for excellent and exciting scientific endeavours. iNEXT (http://www.inext-eu.org <http://www.inext-eu.org/>) is committed to bring structural methods closer to non-experts, by funding access to world class infrastructures for Structural Biology. Major tools for achieving that goal are the so-called Extended Support modalities. We are happy to announce the start for acess to the iNEXT Enhanced Support modality for NMR (NMR assignment, structure, dynamics). In this mode, the NMR groups in Florence, Frankfurt and Utrecht are involved in guiding and training NMR novices. This iNEXT access modality also targets "new users with backgrounds other than Structural Biology”, so please feel free to forward that also to your biochemistry friends. Facility personnel will be involved to guide assignments, titrations, structure calculations, relaxation analyses, etc. I also want to bring your attention to a few more iNEXT news: - The Structural Audit, now allows multiple samples in a related project to be submitted in a single application for stability assessment and crystallisation screening; a basic analysis by SAXS, EM, or NMR is also supported (single click in application!) if an appropriate sample is available. - The Enhanced Support modality "From macromolecular sample to X-ray data collection” is now better integrated with Structural Audit; applications can be combined, so in case of a successful Audit, you could rapidly proceed to further X-ray experiments (crystal optimisation, SAXS and/or crystallography) - The Enhanced Support modality "Advanced light imaging” to support structural studies with in cells measurement of protein interaction kinetics, have also been made recently available. - The Enhanced Support modality "Cryo-EM sample optimisation” for hands-on assistance in optimizing a sample for single particle EM is a great chance to move your sample towards cryo-EM! - The Enhanced Support modality "Macromolecular interactions” is your chance for access to a Biophysics facility with various instruments and hands-on support for performing and analysing experiments to quantify a variety of interactions. - All the High-End modalities (X-rays, NMR, cryo-EM) are always open for access! So, please, submit your proposal now! <https://www.structuralbiology.eu/update/submit-proposal?t=inext> … and keep in mind that a limited amount of the funding (~10%) can go towards projects that are not in an EU-country or associated country. On behalf of the iNEXT Management, Best wishes, Tassos Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

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phenix.real_space_refine crashes for very large pdb files
by #AHMED TOFAYEL# 01 Dec '16

01 Dec '16

Dear developers and users, My phenix.real_space_refine run crashes with the error mentioned below when I have used following command to run it on a complete ribosome (containing coordinates for small subunit and large subunit in a single pdb file): phenix.real_space_refine model.pdb map.mrc resolution=4.5 reference_coordinate_restraints.enabled=true reference_coordinate_restraints.selection="chain A and resseq 2:700" reference_coordinate_restraints.sigma=0.05 secondary_structure.enabled=True res.eff > out.out >From the out.out file I can see that, it ran for 5 macro_cycles and started group b-factor refinement which reads (last few lines): |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.144348 restraints weight = 1067.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147257 restraints weight = 482.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.149066 restraints weight = 262.900| |-----------------------------------------------------------------------------| The run crashes at this point.... However, phenix.real_space_refine runs fine when I am refining a protein chain or a complex (for eg: just the large or the small subunit of a ribosome). Does it have to do with my pdb file being so big after merging of both subunits where I have also crossed 99999 atoms and atom serial numbers start from A0000? A related question: What is the latest consensus of using chain IDs and atom serial numbers to use in phenix.real_space_refine for handling large files like ribosome pdbs ? I have found some information on: http://cci.lbl.gov/hybrid_36/ The error in terminal reads: Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 782, in <module> o = run(sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 518, in __init__ self.caller(func = self.run_macro_cycles, prefix="Macro-cycles") File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 547, in caller status = func(prefix=prefix, **kwargs) File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 540, in run_macro_cycles log = self.log) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 66, in __init__ self.caller(self.refine_adp, "ADP refinement") File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 71, in caller status = func(prefix=prefix) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 317, in refine_adp adp_refinery.refine() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 78, in refine b_isos_refined = self.refine_box_with_selected(selection=sel) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 56, in refine_box_with_selected fmodel.update_all_scales(update_f_part1=False, apply_back_trace=True) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1452, in update_all_scales self.apply_scale_k1_to_f_obs() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1500, in apply_scale_k1_to_f_obs r_start = self.r_work() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2004, in r_work selection = selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1972, in _r_factor f_model = self.f_model_scaled_with_k1_w().data() File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1730, in f_model_scaled_with_k1_w data = self.scale_k1_w()*self.f_model_work().data()) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2048, in scale_k1_w selection=selection) File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 182, in _scale_helper raise RuntimeError("Zero denominator in scale calculation.") RuntimeError: Zero denominator in scale calculation. Best regards, Tofayel

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difference map based on the cryo-EM map
by Smith Lee 01 Dec '16

01 Dec '16

Dear All, Supposed by phenix.real_space_refine I got a PDB of protein-ligand, will you please let me know how to get the subtraction map (difference map?) which only show the density of the ligand, so that I can see whether the ligand was well resolved in the map, or whether the built ligand fits well with the ligand density? Smith

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Incrementing high resolution cutoff in phenix.mtz2map or phenix.cut_out_density
by Andrew Morin 30 Nov '16

30 Nov '16

Hello, I am trying to find a convenient way to generate maps using phenix.mtz2map at increasingly greater values of d_min. For example: I have a .mtz file of a structure solved at 2.4A. I run phenix.mtz2map with d_min=none and obtain a map using all of the resolution data. I would like to also create 10 more maps with d_min = 3.4, 4.4, 5.4, 6.4,...12.4A. An mtz of 1.7A would increment at 2.7, 3.7...11.7A, etc. Might anyone know of a handy way to automate this over a large number of mtz files? ALTERNATIVELY - I am performing a phenix.cut_out_density step prior to this. So if it might be easier to automate a incrementing high resolution cutoff in phenix.cut_out_density, that would also work. Thanks for your help. -Andrew

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Refine only selective chains in a complex using phenix.real_space_refine
by #AHMED TOFAYEL# 30 Nov '16

30 Nov '16

Dear all, Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex. During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line. Best regards, Tofayel NTU Singapore

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Can't Run Rosetta_refine
by NISHANT SINGH 29 Nov '16

29 Nov '16

Hi Everyone, I am trying to run Phenix's rosetta refine. I seem to have downloaded and compiled the rosetta package fine, as I got the following statement after compiling was done: scons: done building targets. but I am failing at running: rosetta.build_phenix_interface. It says that command not found. I am attaching my env page with this email. bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$ env ROSETTA3_DB=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/database TERM_PROGRAM=Apple_Terminal SHELL=/bin/bash TERM=xterm-256color TMPDIR=/var/folders/cb/5v492std3d31jr42j7h3jm9h0000gp/T/ Apple_PubSub_Socket_Render=/private/tmp/com.apple.launchd.KEC4L2Cjos/Render TERM_PROGRAM_VERSION=387 OLDPWD=/Applications TERM_SESSION_ID=A82EA51D-0920-4F3B-BE03-92AE0C40A44B USER=Kumar SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.tMihawGOC7/Listeners __CF_USER_TEXT_ENCODING=0x1F6:0x0:0x0 ROSETTA_BIN=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH//main/source/bin PATH=/Library/Frameworks/Python.framework/Versions/3.5/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/Users/Kumar/miniconda2/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin PWD=/Applications/rosetta_bin_mac_2016.32.58837_bundle LANG=en_US.UTF-8 XPC_FLAGS=0x0 XPC_SERVICE_NAME=0 SHLVL=1 HOME=/Users/Kumar LOGNAME=Kumar DISPLAY=/private/tmp/com.apple.launchd.BhETYwyInl/org.macosforge.xquartz:0 PHENIX_ROSETTA_PATH=/Applications/rosetta_bin_mac_2016.32.58837_bundle/PHENIX_ROSETTA_PATH/ _=/usr/bin/env bmbs-imac:rosetta_bin_mac_2016.32.58837_bundle Kumar$

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kickmaps
by Veronica Fiorentino 25 Nov '16

25 Nov '16

Dear all, I am using the latest Phenix; Calculate Maps does not seem to have an option to for kickmaps as given in the https://www.phenix-online.org/documentation/reference/create_maps.html I have made a screenshot: http://imgur.com/a/upgqy Am I missing something obvious? Alternately, If anyone can share a script I would prefer it! many thanks Veronica

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ensemble refinement crash.
by Rajendra Sharma 24 Nov '16

24 Nov '16

Dear all, I am running ensemble refinement using phenix-1.10. The calculations are running good until the Ensemble reducer where the jobs get killed in some cases automatically without giving output pdb. I am using default setting to run the jobs. pdb_stored_per_block is 50 totaling 500 towards the end. Is the crash happening because of memory? Will reducing the number of pdb per block help? Secondly, how can I restart the killed runs? thanks in advance. Raji *Rajendra SharmaResearch Scholar, PhD.* *Centro Nacional de Biotecnología <http://www.cnb.csic.es/>,* *Universidad Autónoma de Madrid,* *Madrid, Spain.Mobile No. +31-656688390*

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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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Postdoctoral positions at the NIH in structural and mechanistic studies on integral membrane proteins
by Anirban Banerjee 19 Nov '16

19 Nov '16

Position Description: The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography with biophysical and biochemical methods such as reconstitution based biochemistry, electrophysiology together with synthetic chemistry to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). We also have an affiliation to the National Institute of Neurological Disorders and Stroke (NINDS). Qualifications: The candidates should hold a Ph. D. degree, be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or insect/mammalian expression systems will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. To Apply: Interested candidates can send an e-mail to anirban.banerjee(a)nih.gov with a CV and a summary of previous research experience and future interests.

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 18 Nov '16

18 Nov '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the January 2017 issue is 15 December 2016. However, if you have a brilliant idea during your holiday break please don't hesitate to forward it. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. 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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gtk glib error messages and too large fonts when starting phenix 1.11.1-2575
by Martin Moche 18 Nov '16

18 Nov '16

Dear colleagues, Today I install latest stable phenix 1.11.1-2575 without problems - output attached. When starting the phenix GUI, the fonts are too large and I get a lot of Gtk, GLib error messages - see below These error messages can be found online as well https://mail.gnome.org/archives/meld-list/2015-January/msg00007.html and are therefore likely not related to phenix. Perhaps somebody knows how to get rid of them and get smaller fonts into phenix GUI? Best regards, Martin ############### my Glib Gtk error messages ############## [x_marmo@triolith2 ~]$ phenix (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:60858): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:60858): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:60858): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:60858): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed Already checked for new versions in last 24 hours, skipping Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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Sorry: Refinement of multiple models not implemented.
by Murpholino Peligro 17 Nov '16

17 Nov '16

I was looking at pdb 2d6b and I try to do a refinement with phenix. (First I generated the cif file with phenix.elbow for 202 ( https://www3.rcsb.org/ligand/202). Then I retry the refinement and I got the error "Sorry: Refinement of multiple models not implemented." How to proceed? Thanks MP

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Why can't I use bootstrap.py in cctbx to compile phenix?
by Taimin Yang 16 Nov '16

16 Nov '16

Dear Professor, My name is Taimin Yang and I am a PhD student in Stockholm University. I try to compile my own phenix using bootstrap.py but here is the error information: root@Linux-main:/usr/local/crystallography_software/phenix# python bootstrap.py --builder=phenix --with-python=/usr/local/anaconda2/bin/python hot update build Performing actions: hot update build Traceback (most recent call last): File "bootstrap.py", line 2034, in <module> run() File "bootstrap.py", line 2029, in run enable_shared=options.enable_shared, File "bootstrap.py", line 926, in __init__ map(self.add_module, self.get_codebases()) File "bootstrap.py", line 1051, in add_module action = MODULES.get_module(module)().get_url(auth=self.get_auth()) File "bootstrap.py", line 553, in get_url raise Exception('No anonymous access method defined for module: %s. Try with --%s'%(self.module, e.args[0])) Exception: No anonymous access method defined for module: chem_data. Try with --cciuser What should I do to compile my own phenix? Thank you very much. Best regards, Taimin

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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. ******************************************************************

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phenix fails to configure on fedora 20
by abhisek Mondal 03 Nov '16

03 Nov '16

Hi, I'm using Fedora 20 on a 4 core laptop. When I tried to install phenix it gave following error. Same version installed fine in my workstation but keep failing here. Please help me out here. Thanks. *[root@viralhost phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6]# ./install * * ==========================================================================* * Phenix Installation* * version: 1.10.1-2155* * machine type: intel-linux-2.6* * OS version: 3.19.8-100.fc20.i686* * destination: /usr/local/phenix-1.10.1-2155* * # of processors: 4* * =========================================================================* *Configuring Phenix components...* *Traceback (most recent call last):* * File "./bin/install.py", line 262, in <module>* * installer(sys.argv[1:]).install()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install* * self.install_from_binary()* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary* * self.reconfigure(log=log)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure* * call(args=args, log=log, verbose=self.options.verbose)* * File "/home/abhisek/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 81, in call* * raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc))* *RuntimeError: Call to '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 126* -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA*

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