- phenixbb - phenix-online.org

seeking advice on how to configure Phaser-MR (full-featured) to use a previous partial solution
by Emilia C. Arturo (Emily) 08 Aug '17

08 Aug '17

Hello. I have a 3-domain protein (let's say it's organized from N to C as A-B-C) whose structure I am working to determine now. Although several single- (A alone, B alone), double- (A+B and B+C) and 3-domain (A+B+C) structures of this protein (from a different organism whose primary sequence is, overall, ~85% identical to the one on which I'm working) have already been determined and deposited in the PDB, I would ideally like to use a minimal probe (i.e. as few domains as possible) in order avoid model bias that could be imposed on the relative orientation of domains A, B, and C. So far, I have phase solutions (TFZ scores for all in the high-50s and 60s) using B-only, A+B, and B+C pdb files as probes. A-only structures have not given a phase solution (TFZ is ~7 and autobuild gives a solution that looks unbelievable in Coot), perhaps because A is relatively small in size. Here is my problem: I suspect that A and B sit relative to one another in an interesting way in this particular structure, so I'd like to use Phaser to search for a solution given the fixed partial solution from a B-only search, together with an A-only structure as a separate probe. So far no MR solutions have been found when I configure the run with an A-only pdb file and a B-only-derived Phaser result that is input as a fixed partial solution. I'm writing to ask for advice on how to configure the search. I think that the problem is my configuring the search, and not that a solution cannot be found from these coordinates. This is the reason I think that my problem is in configuring the search; please correct me if I'm wrong: Using a Phaser result derived from using an A+B structure as probe, I cut up the resulting pdb file into 2 pdb files - one containing an A' and another containing a B', where A' is the A domain of the Phaser result, and B' is the B-only part. Then I configured a Phaser result with B' as an ensemble that is a fixed partial solution, and A' as a separate ensemble/probe. I searched for 4 of each since 4 chains is the most likely composition in the ASU. I expected to get a result similar to what Phaser calculated when I input the A+B structure as an intact probe. Instead of getting a solution where 4 A+B chains were placed as they were in the first Phaser result, which gave one solution with a TFZ score of 65, I got 13 solutions, the top scoring a TFZ of 7.5, and each solution having a total of 9 chains - 4 As and 5 Bs. Is anyone willing to help me troubleshoot the above before I throw up my hands and settle on either manually building two domains onto the single-domain solution, or one domain onto the 2-domain solution, keeping in mind the potential for model bias? I am keen on using the B-only solution as a fixed partial solution to place domain A because all the B-only structures provide coordinate information for a portion of domain B that is unresolved in any of the multi-domain structures that contain domain B. I am using the Phenix gui, version 1.12rc1-2807. Regards, Emily. -- "Study as if you were going to live forever; live as if you were going to die tomorrow." - Maria Mitchell "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May Alcott

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Very low rmsd bond length
by Mark Saper 07 Aug '17

07 Aug '17

Hi all, A reviewer points out that my refined structures (which have already been deposited in PDB) have very small RMSD values for bond lengths (0.005–0.002) (refinement resolutions are 2.0–2.8 Å), and that my weights should be decreased. The weights were calculated with “Optimize XYZ Weight” option turned ON. This seems to be the case with all of the structures that I have refined during the past 5 years. My impression from previous discussions is that deriving explicit weights from these optimized ones is not straightforward and so I have never tried to relax the weights. Moreover inspecting the optimization results in the log file, suggest that changing the weights to increase the RMSD would increase the Rfree. (I can post this if its helpful). How do I address the reviewer’s concerns? Thanks, Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School Room 3220B, MSRB III saper(a)umich.edu +1 (734) 764-3353

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Comput. Cryst. Newsl. (2017) 2
by Nigel Moriarty 05 Aug '17

05 Aug '17

The latest Computational Crystallography Newsletter is available for download. Below is the clickable table of contents. July 2017 <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf> Short Communications - phenix.mtriage: a tool for analysis and validation of cryo-EM 3D reconstructions <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=6> - More TLS validation with phenix.tls_analysis <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=8> Fitting tips #14 – How Ser & Thr behave oddly on helices <https://www.phenix-online.org/newsletter/CCN_2017_07.pdf#page=2> 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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mrc to mtz conversion to open map in coot
by Joshua Jude Lobo 03 Aug '17

03 Aug '17

Hi phenixbb I am new to phenix and am trying to convert a cryo-em map(mrc format) to mtz format using the phenix.map_to_structure_factors command .This proceess finishes without errors but the resultant mtz file is not viewable in coot . I have tried both the phenix.map_to_model and the phenix.map_to_model_histogram_1.12-2829 How is the best way to troubleshoot this ? Any inputs would be appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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Berkeley servers are back in service
by Billy Poon 03 Aug '17

03 Aug '17

Hi everybody, The servers at Berkeley are now available. Please let us know of any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Lab Evac
by Nigel Moriarty 03 Aug '17

03 Aug '17

Folks The Grizzly Fire (the media loves a interesting name) is more than 50% contained and the lab is now open. The servers are, once again, available for downloading the latest version of Phenix, 1.12. 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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Emergency shutdown
by Nigel Moriarty 02 Aug '17

02 Aug '17

Folks Phenix servers are shutting down due to a grass fire in the area. 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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Postdoctoral position in Structure and Function of Fungal Membrane Proteins
by Maike Bublitz 02 Aug '17

02 Aug '17

Postdoctoral position in Structure and Function of Fungal Membrane Proteins A post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of fungal membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage. To apply for this role and for further details, including the job description and selection criteria, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Applications for this vacancy are to be made online by 31th August 2017.

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(no subject)
by Priyanka Abeyrathne 21 Jul '17

21 Jul '17

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Phenix version 1.12 released
by Paul Adams 14 Jul '17

14 Jul '17

The Phenix developers are pleased to announce that version 1.12 of Phenix is now available (build 1.12-2829). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: New tools for secondary structure validation, comparing multiple related structures, cryo-EM model and map validation, and calculation of real space difference maps. Video tutorials are now available on the new Phenix Tutorial YouTube channel (www.youtube.com/c/phenixtutorials). A suite of tools for cryo-EM model building and structure refinement including automated map sharpening, segmentation, and model building. Real space refinement now has an option to use histogram equalized map as a refinement target. Phaser version 2.8 has several new features, including unit cell refinement for EM data, more extensive use of eLLG in decision making and analysis, anomalous substructure determination (Phassade), improved tNCS detection and analysis, and improvements to SCEDS. - NEW TOOLS - phenix.secondary_structure_validation - tool to validate secondary structure section in .pdb and .mmcif files with option to filter bad annotations. - Structure Comparison: tool for parallel validation and analysis of near-identical protein structures. Results include the analysis of ligands, rotamers, Ramachandran angles, missing atoms, water locations and B-factors. - phenix.mtriage: command-line tool to validate cryo-EM models. GUI is available. Computes various map statistics including resolution estimates, FSC between half-maps, full and model maps. Outputs mask file used to compute FSC. Still under development. - phenix.real_space_diff_map: command-line tool to compute difference map. This is a real-space analogue of Fo-Fc map mainly designed for cryo-EM maps. See http://phenix-online.org/newsletter/CCN_2017_01.pdf for details. - PHENIX VIDEO TUTORIALS Video tutorials about Phenix tools are now available on the Phenix Tutorial YouTube channel (www.youtube.com/c/phenixtutorials). The following topics are covered: - How to run phenix.refine - How to calculate polder maps - How to run phenix.real_space_refine - How to run PDB tools - How to change phenix.refine parameters via the GUI - Basic Phenix eLBOW tutorial - How to run Phaser-MR from the Phenix GUI - Explaining the atom selection syntax - How to run Structure Comparison - NEW FEATURES - Phenix.auto_sharpen: New map sharpening algorithms available based on (1) optimization of map clarity (adjusted surface area or kurtosis), (2) resolution-dependent map-model correlation, (3) resolution-dependent half-map correlation, and (4) local map sharpening - Phenix.map_to_model: Iterative map improvement using model from one cycle to optimize sharpening of the map for the next cycle - Phenix.map_to_object: Now you can individually map each member of a group of chains onto your target - Phenix.chain_comparison: Now can compare a target to each of a group of models - Phenix.find_alt_orig_sym_mate: Now uses ssmalignment.stats to see what residue pairs were included by ssm in a hypothetical calculation of the ssm-rmsd. This is to avoid including atoms that even for an optimal structural alignmentwould have been too far apart that ssm would use them. Excluding these is necessary to avoid having the calculated rmsd blow up. - Now using angles for restraining hydrogen bonds in alpha helices and beta sheets in secondary structure restraints. - Phenix.polder: New option (compute_box=True) to compute a difference map excluding the bulk solvent mask within a user-defined box. The map can be used to inspect interesting difference density peaks. - phenix.map_model_cc (phenix.model_map_cc): various enhancements and bug fixes. - phenix.real_space_refine: - improved ADP refinement (still group) - improved NCS constraints definition - multi-model PDB file is not output by default anymore - (experimental) option to use masked histogram equalized map as refinement target. Using such map dramatically improves refined model geometry. This map is not suitable for ADP refinement. - show CCmask, CCvolume and CCpeaks that report on local and gloabal model to map fit. - RESTRAINTS - Specialised restraints for ligands with differing chemistry in the same model allows using the same 3-letter code but different restraints for a specific instance - apply_cif_restraints - Detailed control of peptide planes and omega angles - apply_all_trans - apply_peptide_plane - apply_cis_trans_specification: use an atom selection (CA) to force a cis or trans omega angle - REEL - Improvements to robustness and features - GUI - New interfaces - phenix.mtriage - phenix.map_box - phenix.auto_sharpen - phenix.map_to_model - phenix.ncs_average (under "Other Tools") - phenix.sculpt_ensemble (alpha) - Updated interfaces - Comprehensive Validation shows real-space correlations from phenix.map_model_cc when map files are used - Structure Comparison - Validation - improved speed of clashscore validation - bug fix to handling of cis-peptides in ramalyze - contours for ramalyze, rotalyze, and cablam now accessible at https://github.com/rlabduke/reference_data - validation GUI now shows altloc identifirs for most outliers - improved internal code accessibility of validation statistics - Phaser-2.8.0 - refinement of cell for data (electron micrcoscopy) - more analysis using eLLG for component addition - more analysis using eLLG for polyalanine residues for target eLLG given rms - more analysis using eLLG for single atoms more ordered than average - more analysis using eLLG for chains/gyre-and-gimble * Phassade: Fast Fourier Transform Anomalous Substructure Determination - SOLU TRIAL records RF-LLG for trial orientation - gyre and translation function report RF recorded for trial orientations - 'scons --ccp4' command line flag for ccp4 build (generates ccp4-style headers) * improved tNCS detection and analysis * gyre and gimble improved for output and python scripting * NMA outputs all perturbed files in MODEL delimited pdb file '<fileroot>.nma.pdb' * sceds outputs domains to chain delimited file '<fileroot>.nma.pdb' - sceds domain pdb file have TER separated domains - NMA option to output separate pdb files for each perturbation (XYZOUT NMA ALL OFF) - sceds option to output separate pdb files for each domain (XYZOUT NMA ALL OFF) - NMA has option to turn off output of input coordinates (NMA ORIG ON) - pdb chain identifies can be left unchanged from input (XYZOUT CHAIN COPY) (for Eleanor) - bugfixes -- allow peaks and purge percent to override one another if not default -- rms estimation developer options not being set correctly -- throw out of memory error if Patterson map allocation fails For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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