- phenixbb - phenix-online.org

Gold atoms in cryo-EM
by a.malay＠riken.jp 12 Sep '17

12 Sep '17

Dear all, I hope that this question is neither too off-topic or naive. I am trying to refine a large protein structure against a cryo-EM map using Phenix real-space refinement. The protein complex is unusual in that the oligomeric state is held together via coordinated gold atoms. However, there seems to be a problem with refinement, in that the the gold atoms show extremely high B-factors (>200) after refinement, whereas the B-factors of the protein residues, including those surrounding the gold atoms, adopt more reasonable values. My question is: could the unusually high B-factors of the gold atoms be somehow due to differences in the relative scattering of Au atoms when obtained from X-ray vs. electron beam irradiation? And if so, is there any way to correct for this? Thank you in advance for your kind help. Best, Ali

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SLURM Batch submission
by Heidi Schubert 11 Sep '17

11 Sep '17

Hi Has anyone successful submitted phenix jobs to a SLURM batch queue? I guess, in theory, I did successfully submit a job but it took a while to start and after completion the log files did not successfully link back to the interface losing the graphic feedback. I can’t tell how the job was submitted. Our submission command is sbatch, which is what I put in the Phenix Preference > Processes queue command. But locally we have a header on our sbatch submission which spells out our wall time, account and MPI expectations/requests. Is there an environment file that Phenix reads to provide this information or does it submit generically? I wondered if this was responsible for the long delay of the start of our job (sure – could have been a busy queue). Anyone know how to get the GUI to read the output files when it loses connection to the run? Heidi

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Resolution of datasets for using PHENIX automated ligand identification
by Xiao Lei 01 Sep '17

01 Sep '17

Hi All, I am asking is there any resolution requirement for using the PHENIX automated ligand identification tool. Can I use the tool with 3A resolution protein datasets?

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.hhr files?
by Patrick Loll 01 Sep '17

01 Sep '17

This feels like a silly question, but I’ve already wasted some time head-banging, so here goes: I would like to generate a .hhr sequence alignment file for use in MR-Rosetta. After running HHPRED, I get a lovely alignment, but I see no place to save it as a .hhr file. Several “how-to” pages talk about a “save” button above the alignment, but the MPI bioinformatics pages seem to have been reformatted in the past few months, and I see no such button. There is a tab labeled “raw output” with a download option, but that appears to give a FASTA format. So…can anyone suggest a way forward? Either by capturing the elusive .hhr file, or by saving the data in some other format that is still useful for MR-Rosetta? Thanks, Pat --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjloll(a)gmail.com pjl28(a)drexel.edu

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Few questions about the model building and refinement of cryo-EM data
by Wang, Bing 28 Aug '17

28 Aug '17

Hi guys, Sorry for the detailed questions from a beginner! I am starting a modeling/refinement work for a set of cryo-EM data. Data basic information: phage data (looks like a ball with P1 space group), map size ~870 MB, resolution ~6 A, two X-ray structures for model building General strategies: I select COOT for the model building; using phenix.real_sapce_refine for the real space refinement with secondary structure restrain and REFMAC for the reciprocal space refinement. Few questions are listed here. 1. The map was too bigger to open it in COOT. The phenix.map_to_structure_factors was used to obtaine ~120 MB sized MTZ file (still a little big for my computer). I manually build up the whole ball-shaped phage with the rigid body fit in COOT (from two X-ray structures to 120 chains). My first question will be: In this case, should I crop the map in Chimera or other software and only focus on a small asymmetric unit to do the model building and the followed refinement. 2. I would like to do a real space refinement after the model building. Input files: A pdb file I just built up from COOT A original MAP file A transfered MTZ file Two restraint files from two X-ray structures by ProSMART (TXT formart) The refinement parameters I would like to select in GUI interface: minimization_global, rigid_body, local_grid_search, adp Use secondary structure restraints Reference model restraints: use starting model as reference, main chain, side chain, fix outliers, secondary structure only Rotamer restraints Ramachandran restraints Show per residue My second set of questions: Should I select the MAP file (~870 MB) or the MTZ file (~120 MB)? Is that necessary to add the two restraint files from ProSMART if I use the starting model as reference? Is the refinement parameters selected properly? 3. I gave a try by phenix.real_space_refine. An first error showed up: Number of atoms with unknown nonbonded energy type symbols: 6840 "ATOM 184 HG1 SER 1 12 .*. H " "ATOM 458 HG1 SER 1 30 .*. H " "ATOM 699 HG1 SER 1 45 .*. H " "ATOM 720 HG1 SER 1 47 .*. H " "ATOM 762 HG1 SER 1 50 .*. H " "ATOM 1241 HG1 SER 1 81 .*. H " "ATOM 1465 HG1 SER 1 95 .*. H " "ATOM 1747 HG1 SER 1 113 .*. H " "ATOM 1758 HG1 SER 1 114 .*. H " "ATOM 2173 HG1 SER 1 141 .*. H " ... (remaining 6830 not shown) I tried phenix.ready_set to fix this problem according to a previous discussion but it gave me another error: ENDMDL record missing at end of input. Thus my third question will be how to fix the first error? Thank you for patience! I would really appreciate your help! Bing

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Opening phenix X-ray/neutron maps in Coot without the Phenix GUI
by Derek Logan 23 Aug '17

23 Aug '17

Hi ccp4bb and phenixbb, Is there a convenient way to open MTZ files in Coot that are the result of joint X-ray/neutron refinement in phenix.refine, but where phenix.refine was run in command-line mode? I would like achieve what is done in the Phenix GUI at the click of a button, i.e. open Coot with the structure and 2Fo-Fc and Fo-Fc maps for both neutron and X-ray. At the moment I have to open each MTZ file four times in the Coot GUI, once for each type of map. Is there a script buried somewhere in the Phenix installation that can be modified? /Derek ________________________________________________________________________ Derek Logan tel: +46 46 222 1443 Associate Professor mob: +46 76 8585 707 Dept. of Biochemistry and Structural Biology www.cmps.lu.se<http://www.cmps.lu.se> Centre for Molecular Protein Science bit.ly/2d0HxmS Lund University, Box 124, 221 00 Lund, Sweden

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Master Your Proteins, NKI Amsterdam, 20-23 November 2017
by Anastassis Perrakis 18 Aug '17

18 Aug '17

Dear all, Applications for the Instruct-ERIC course on Biophysical Characterisation of Macromolecules and Quantification of Biomolecular Interactions are now open. The course aims to provide the theoretical background of popular biophysical methods that are often used in relation to Structural Biology research, and practical experience both in performing experiments and in analysing the resulting data. The rationale behind an extended kit of experiments to characterise macromolecules and their interactions will be explained. You will be shown how to perform and analyse the related experiments in dedicated practical sessions. The course will include theory and practical sessions on thermal shift assays (also label free), Surface Plasmon Resonance, sothermal Titration Calorimetry, Miscroscale Thermophoresis , Fluoresence Methods, Stopped Flow, and the Graphpad/Prism and Kintek analysis software. Details can be found at: https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac… <https://www.structuralbiology.eu/events/biophysical-characterisation-of-mac…> On the behalf of the organisers, Tassos

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Macromolecular Crystallography workshop in South America
by Alejandro Buschiazzo 18 Aug '17

18 Aug '17

Dear colleagues, We are pleased to announce our sixth edition of the Workshop: Macromolecular Crystallography School "From data processing to structure refinement and beyond", to be held at the Institut Pasteur de Montevideo (Uruguay). http://pasteur.uy/mx2017 Dates: November 13 - 23, 2017 Confirmed speakers and tutors (so far... a few more may join the crew): Alejandro Buschiazzo, Montevideo, Uruguay Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil Ronan Keegan, Oxford, UK Eugene Krissinel, Oxford, UK Andrey Lebedev, Oxford, UK Andrew Leslie, Cambridge, UK Garib Murshudov, Cambridge, UK Colin Palmer, Oxford, UK James Parkhurst, Oxford, UK Randy Read, Cambridge, UK Clemens Vonrhein, Cambridge, UK Please find the program of the Workshop, the application form and further contact information, at http://pasteur.uy/mx2017 (this www site will be updated regularly, so stay tuned!) This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); the International Union of Crystallography (IUCr); and the Institut Pasteur de Montevideo. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Ronan Keegan, PhD. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 24 students will be selected, aiming at advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site for details on application procedures. The application deadline is September 17, 2017. Please address further inquiries to: mx2017(a)pasteur.edu.uy Looking forward to welcoming you in Montevideo! -- Alejandro Buschiazzo, PhD Associate Professor Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…

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Postdoctoral position at the University of Chicago
by Robert Keenan 15 Aug '17

15 Aug '17

The Keenan lab at the University of Chicago has an opening for a postdoctoral scientist to study the structure and function of protein complexes involved in membrane protein biogenesis and quality control. Applicants should be nearing completion of a PhD in structural biology and have a strong academic record with significant publications. Experience in molecular biology, protein purification and electron microscopy/x-ray crystallography is required. To apply, please send a CV and a short statement describing your motivation for wanting to join the lab. Please be prepared to arrange for three letters of reference to be sent by email. For more information, please visit our webpage: http://keenanlab.bsd.uchicago.edu

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Phenix.real_space_refine
by Reza Khayat 11 Aug '17

11 Aug '17

Hi, I am refining a virus into an image reconstruction and have been having issues using the NCS capability of phenix.real_space_refine_1.12-2829. I think it may be my misunderstanding of the manual. The virus has 60subunits and I am feeding phenix a complete oligomer. I manually modify the first subunit with coot (simple movements and such), define an NCS group file where the first subunit is the reference and the other 59 are selection, and feed these into phenix.real_space_refine. Does phenix recapitulate my modifications of the first subunit into the remaining 59 subunits to create an oligomer that contains all my modifications before starting refinement? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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Appplying symmetry to a Cryo-EM map in phenix map_to _model
by Joshua Jude Lobo 11 Aug '17

11 Aug '17

Hi Phenix Group I am very new to model building and using phenix . I am trying to use phenix.map_to_model to generate a model just using my cryo-EM map( mrc format) and a fasta sequence .My protein has octahedral symmetry . I found the use_space_group_symmetry argument but am not sure what argument to give to impose the symmetry . Any inputs are appreciated Sincerely Joshua Lobo University of Minnesota Twin Cities

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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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Problem with smiles string in elbow
by Edward A. Berry 14 Jul '17

14 Jul '17

I'm not getting the expected result with this string: COC(=O)C(=COC)c1ccccc1COC(N1C)=CC(=N1)C(=C2O)C=C(Cl)C=C2 When used with coot Lidia it gives the expected result (upper picture). But when I run elbow like this: phenix.elbow --smiles="COC(=O)C(=COC)c1ccccc1COC(N1C)=CC(=N1)C(=C2O)C=C(Cl)C=C2" --output="Y7303" --id="Y03" the result is the lower picture. In particular the pyrazole ring (arrow) gets distorted, but other bond lengths are way off. I want to use elbow because it names the atoms as numbered in the order they appear in the smiles string, irrespective of the element. This is good because this is one of a series of compounds in some of which C's are replaced by N's and vice versa so it helps to have the same number for atoms in the same position. What does work is to save the structure as .mol from Lidia and feed that to elbow, which gives the right structure and the elbow atom names. But it would be good to find out why it isn't working directly. my elbow is: electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.12rc1-2801 None

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Problem with rotamer refinement
by Renato Ferras 11 Jul '17

11 Jul '17

Dear all, I am refining a protein structure at 1.74 A resolution with phenix.refine (version 1.10.1_2155) and I have noticed that some side chains don't remain in the electronic density even after careful hand adjustment in which they are almost perfect. It seems pretty clear where the side chain should (must) be located, moreover it is consistent with two rotamers (either rotamer tp60 - #4 in coot - or rotamer tp-100 - #9 in coot -, which are approx. at 180 deg for chi3). In spite of that, after reciprocal space refinement, I observe that the end of side chain rotates chi3 angle and both N and O gets far from where they started (there is this difference in the chi3 angle). My concerns are about the proper interpretation of geometrical restraints listed in .geo file, specially what the ideal value is, how weights are applied to ideal value and why phenix doesn't reach convergence in reciprocal space refinement. Below are the values from .geo for the referred Gln: dihedral pdb=" CB GLN B 21 " pdb=" CG GLN B 21 " pdb=" CD GLN B 21 " pdb=" OE1 GLN B 21 " ideal model delta sinusoidal sigma weight residual 0.00 23.41 -23.41 2 3.00e+01 1.11e-03 8.42e-01 is there a description for us to interpret what these numbers are? To my understanding, the ideal values are established as being either 0 or 180 degrees (yet sinusoidal 2). I cannot say about how heavy the weights are on these (in fact, I left my refinement to optimize weights), but anyway, if I understand correctly, the ideal value (for chi3) should be rotamer dependent. Taking Gln as an example, I see several rotamers do have values close to either 0 or 180 degree, but what about rotamers 4 and 9? I might imagine a similar situation for residues like Asn and His, though I have not searched deep for these yet. Thanks, Renato

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crystal imaging system
by Sebastiano Pasqualato 30 Jun '17

30 Jun '17

Dear all, we are in the process of considering the purchase of a new Crystal Imager. So far, we have been considering the Formulatrix Rock Imager 182 and the TriTek Crystal Pro HT. I would be extremely grateful to anyone who could provide me: - feedback and user experience (positive/negative) on those instruments; - information on other instruments you would suggest. Thank you very much in advance, wishing you a pleasant weekend, best regards, ciao, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit

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Phenix polder error
by Avinash Punekar 26 Jun '17

26 Jun '17

Dear all, When I run phenix.polder through command line, I get a message "Sorry: Multiple equally suitable arrays of observed xray data found." and phenix.polder stops without producing the maps. How to solve this problem? Any help is highly appreciated. Thanks, Avinash

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