- phenixbb - phenix-online.org

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 13 Jul '17

13 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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does phenix refine fill in missing data?
by Ursula Schulze-Gahmen 22 Jun '17

22 Jun '17

I have very anisotropic data. I used the staraniso webserver to analyse and process my data which creates a final merged file with very incomplete data in the outer shells. If I use this data file in Phenix, what will happen? Will Phenix automatically fill in the unobserved data? If so, can I prevent it from doing so? I am importing the data with the reflection file editor and it seems the reflections are being filled in already at this stage. Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491

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Cif file recognition
by Joel Tyndall 21 Jun '17

21 Jun '17

Hi there, Having a few minor issues with my phenix setup on windows 10. I have the latest stable build Phenix1.11.1-2575. When introducing a new ligand that exists in the monomer library, Pheix complains it does not have the geometry restraints (cif file) - somehow it is not seeing its own library. How can I set up the cif library as default? Cheers Joel Joel Tyndall | BSc(Hons) PhD Associate Professor in Medicinal Chemistry School of Pharmacy | Te Kura Mātauraka Wai-whakaora University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Skype: jtyndall Website | pharmacy.otago.ac.nz

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sculptor modifications
by Emilia C. Arturo (Emily) 21 Jun '17

21 Jun '17

Hello All, Is there a way to identify quickly the changes to a model that Sculptor has made? I am running the Phenix GUI to use Sculptor. I have read through the out-put log file, and understand (mostly) the sculpt protocol as it relates to the circumstances under which modifications to main chain or side chains are made, but it would be nice to see (in a list format, perhaps) what changes (if any...) were made. 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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phenix.map_to_model input mtz file failure
by dancingdream＠163.com 18 Jun '17

18 Jun '17

Dear Phenix bb, I intend to build a initial model by phenix.map_to_model. And the command line is as follows: phenix.map_to_model_1.12rc0-2787 map_coeffs_file=../rep_dm.mtz map_coeffs_labels="'FP,SIGFP' 'PHIDM' 'FOMDM'" seq_file=../resolve.seq is_crystal=True use_sg_symmetry=True density_select=False truncate_at_d_min=True and the feedback like this: Sorry: No initial assignment made for map_coeffs. Labels used: FP,SIGFP PHIDM FOMDM. Available labels: ['PHIB', 'FOM', 'HLA,HLB,HLC,HLD', 'FP,SIGFP', 'PHIDM', 'FOMDM', 'FDM', 'HLADM,HLBDM,HLCDM,HLDDM'] NOTE: grouped labels like 'FP,SIGFP' must stay together, have commas, and have no spaces. If they come from an MTZ file, they must be in adjacent columns as well. Suggested labels to use: PHIDM FOMDM I try many other input format of map_coeffs_labels, such as map_coeffs_labels="FP,SIGFP PHIDM FOMDM" map_coeffs_labels=["FP,SIGFP PHIDM FOMDM"] ... ... but the result is the same. Dose anyone can tell me how to fix this problem? Thank a lot. -- Wei Ding P.O.Box 603 The Institute of Physics,Chinese Academy of Sciences Beijing,China 100190 Tel: +86-10-82649083 E-mail: dingwei(a)iphy.ac.cn

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Overall anisotropic ADP in phenix.real_space_refine?
by Oliver Clarke 17 Jun '17

17 Jun '17

Hi, I wonder in phenix.real_space_refine whether it may be worth adding refinement of a single overall anisotropic ADP to the model - or a single TLS group with modeled anisotropic ADPs - in order to model the effects of overall orientation errors (which affect resolution more substantially towards the periphery) and preferred orientation (which tends to give rise to anisotropic resolution across the volume). Maybe this would be helpful at least in generating a calculated map that is better for difference map calculation, for example? Cheers Oli

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real_space_refine questions
by Daniel Larsson 14 Jun '17

14 Jun '17

I'm have some questions about doing real space refinements using phenix.real_space_refine. I am refining a model for an intermediate-resolution (3.79 Å) cryo-EM map. As the starting point I use a model from a higher-resolution map (3.25 Å) of the same system in another conformation. My idea is to first do rigid body fitting of domains and then gradually relax constrains and restraints. - Is it possible to restrain the position of certain parts of the model (i.e. "freeze" them so that they move at all) to do focused refinement of subdomains or loops? - In the instructions it says that you can do both NCS constraints and restraints. How you do the latter? I can only do the former by default or by defining ncs_constraints=True and give a NCS definition file. - When I do a run with run=rigid_body, some rigid body groups move in to each other and overlap. Is there no collision detection using this algorithm? If I do a run=minimization_global, things work a bit better in this regard, but is not really what I want (at this stage). Am I doing something wrong? Here is the run command and the rigid body definition file: phenix.real_space_refine \ model.pdb \ map.ccp4 \ rigid.eff \ resolution=8.0 \ ncs_constraints=False \ rotamer_restraints=True \ ramachandran_restraints=True \ c_beta_restraints=True \ run=rigid_body \ macro_cycles=10 # rigid.eff: refinement { rigid_body { group = chain A and resseq 101:266 group = chain A and resseq 273:388 group = chain B and resseq 101:266 group = chain B and resseq 273:388 group = chain C and resseq 104:266 group = chain C and resseq 273:388 } } Regards, Daniel Larsson

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 13 Jun '17

13 Jun '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the July 2017 issue is 30 June 2017. 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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preparing DL-Malic acid stock solution
by Sebastiano Pasqualato 08 Jun '17

08 Jun '17

Dear all, we’ve recently having trouble preparing a 3 M stock solution of DL-Malic Acid, pH 7 (which we had, so it’s doable!). When we reach pH 3 - 4 the solution turns milky white and does not goes back to a clear solution even when the pH is raised. Does anybody have any advice on how to get a clear solution? Has anyone gone through the same? Thanks in advance, ciao, Sebastiano -- 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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Re: [phenixbb] AutoSol invalid MTZ column_types error
by Terwilliger, Thomas Charles 08 Jun '17

08 Jun '17

Hi Mintu, I'm sorry about this problem! I should have fixed it already but missed this message from Phil Evans that he posted in January: "Columns N(+) and N(-), both of type I, are recent additions to the output file from Aimless. They are the number of observations merged into I(+) and I(-) respectively" AutoSol doesn't know about these columns and can accidentally guess that they are data. To get around this column, use a command like this to create a data file that does not contain the N(+) and N(-) columns: phenix.reflection_file_converter aimless.mtz --mtz=aimless_noN.mtz --label="I(+" ?where the --label=xxxx command specifies the first few characters of the columns you want to use as I+/I- data. Then use aimless_nonN.mtz instead of aimless.mtz as input to autosol. I will fix this in autosol. Let me know if that does not do it! All the best, Tom T Dear all, I am getting an error message "Invalid MTZ column_types for the given miller_array." while I try to run AutoSol. The last line in the log is "Adding array ['N(+)', 'N(-)'] to output file with type II". Do you have any suggestion how to fix this error? Thanks a lot in advance. Best, Mintu

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comfortable OS X level
by Patrick Loll 07 Jun '17

07 Jun '17

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to Sierra? Thanks as always, 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 pat.loll(a)drexelmed.edu

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ligand - protein close contact
by Nikos Pinotsis 06 Jun '17

06 Jun '17

Dear all, I have a protein-ligand structure with several chains in the AU. After refinement one of the ligands forms a close contact 1.8A with the protein. For the rest of the protein-ligand chains the same interaction is as expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with coot but everytime I am getting back the same 1.8 A close contact. There is enough density for the ligand and I can even see that it can fit better to distance 2.4-2.5A H-bond with the protein Is there a way to constrain this distance to more than 2A? Should I fix the ligand atom that interacts? Unless I am missing something more fundamental. The ligand cif file is the default in phenix, the data set is a quite decent 2.3A. thanks in advance for any suggestions Nikos -- Dr. Nikos Pinotsis Institute of Structural and Molecular Biology Department of Biological Sciences, 3rd Floor, R313 Birkbeck College Malet Street London WC1E 7HX T: +44 (0)207 631 6827 F: +44 (0)207 631 6803 M: +44 (0)792 384 3593

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Composite omit map
by Sam Tang 05 Jun '17

05 Jun '17

Dear all Sorry for a very basic question about generating an omit map. I am trying to generate a SA-omit map for only my ligand but not the protein core of my complex. I presume I can use phenix.composite_omit_map GUI and specify my ligand chain in Atom Selection? All other parameters being the same, I notice that when I did not select any atom the whole structure was divided to 30-40 regions but when I selected my ligand chain it now divides into 89 regions. Is there a reason why and is there any advantage to manually adjust the number of omit regions? Many thanks and regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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Fitting ligand with DM map?
by Sam Tang 03 Jun '17

03 Jun '17

Dear community I guess it may not be a standard practice but I wonder if anyone has tried to use a density modified map for ligand building. My situation is that I am trying to fit a single strand DNA ligand into an enzyme model. The dataset is at 3 Ang, P1 space, with overall completeness of only about 88%. MR was done by the apo-enzyme and the density for the first two-third of the ligand is very good and could easily be modelled. Towards the last one-third the density becomes much weaker so nucleotides cannot be easily put. This is the only dataset so far, so multi-crystal averaging / map averaging is not possible at this stage. NCS averaging is also not possible. We did try to sharpen map during refinement. I understand that DM is usually used to improve phase at the initial stage esp. with experimental phasing. With MR would you think density modification could produce a better map to aid the modelling of the last one-third ligand? Can I use the denmod.mtz directly for manual model building? Any input would be very much appreciated. Best Sam Biochemistry Programme, CUHK

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Questions on TLS output and more info on phenix.tls
by Michael Garavito 29 May '17

29 May '17

I am finishing the final stages of refinement with TLS at 1.7 Å and want to begin some B-factor analysis. Also, I am setting up for a series of ensemble refinements. However, I am second guessing myself and have been finding that several basic questions that are not explicitly answered by the Phenix documentation. (1) Just to be sure, I looked for the definition of what is written in the ATOM records of the output PDB file after refinement with TLS: residual B or total B (residual B + TLS contribution). I always thought the latter after refinement with TLS, but nothing was explicitly stated. (2) Also, I have looked for it extensively in the Phenix documentation, I have not found any information on phenix.tls, even though in several places (e.g., phenix.ensemble_refinement), there are explicit references to phenix.tls: “If TLS is used the TLS components must be present in the atom records (see phenix.tls)” The information from just doing % phenix.tls -h does not give enough insight into options and there use. Can someone point me to the right place to get these answers? Thanks, Michael **************************************************************** R. Michael Garavito, Ph.D. Professor of Biochemistry & Molecular Biology 513 Biochemistry Bldg. Michigan State University East Lansing, MI 48824-1319 Office: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334 Email: garavito(a)msu.edu ****************************************************************

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Linking C-Type Heme
by Julian Esselborn 23 May '17

23 May '17

Hi list, that might sound like a stupid question, but we are having some trouble getting phenix.refine acknowledging a c-type linkage of a heme. That is a covalent Cys SG bond to C18 or C25 in the heme. The pdb file does contain a LINK record for this, but Ready Set seems to ignore that even if told to look for LINK records. The distance in the model is actually around 1.9 Ä and automatic ligand linking is on and set well below that distance. Any ideas why this might be failing and what is the smartest way to proceed? Any ideas highly appreciated. Thanks a lot Julian Esselborn Tezcan Lab UC San Diego

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Research Track Assistant Professor Positions
by Diana Tomchick 22 May '17

22 May '17

Assistant Professor, Research Track Department of Biophysics The Structural Biology Laboratory at UT Southwestern Medical Center currently has two openings at the non-tenure track Research Assistant Professor level for highly-motivated individuals who enjoy working in a collaborative, multi-disciplinary setting. · Position #1: Cryo-electron microscopist with extensive experience in high resolution single-particle reconstruction, including sample grid preparation, data collection, the use of modern software for particle picking and classification, map generation, model building and structure validation. Experience in cryo-EM tomography is a plus. · Position #2: X-ray crystallographer with extensive experience in modern methods of crystallization, data collection using home and synchrotron sources, structure solution via various experimental techniques, refinement and structure validation. For both positions, a Ph.D. in biochemistry, chemistry, physics or a related field is required. Facility with related techniques for each position such as cryo-electron microscopy, X-ray crystallography, NMR, small-angle X-ray scattering, isothermal titration calorimetry, analytical ultracentrifugation and protein expression and purification is highly desirable. Job requirements include a significant amount of both formal and informal teaching, and teaching experience is highly desirable. Salary is competitive and commensurate with experience and qualifications. About the UT Southwestern Structural Biology Laboratory The Structural Biology Laboratory (Diana Tomchick, Director) is a platform that allows researchers with different expertise to come together in a collaborative setting and tackle biological problems in a comprehensive way. Our publications are representative of the success of this strategy: http://www3.utsouthwestern.edu/sbl/Publications.html State-of-the-art equipment is currently installed, operational and shared between the members in the Structural Biology community at UT Southwestern. Cryo-EM equipment consists of one 300 kV Titan Krios microscope, one 200 kV Talos Arctica microscope, and a cryo-Scios DualBeam for cryo-FIB milling. In addition, the Structural Biology Laboratory has a dedicated lab for cryo-EM grid preparation, with an FEI Vitrobot and assorted instruments for sample prep. Computational facilities include a campus high-performance computing cluster. Crystallographic equipment includes an Art Robbins Gryphon crystallization robot and a Scorpion liquid handling robot, a Jansi UVEX UV microscope, a Rigaku FRE superbright rotating anode X-ray generator with an ACTOR sample mounting robot, and 30 days of guaranteed synchrotron beam time at Sector 19 of the Advanced Photon Source. These facilities are supplemented by a variety of biophysical instruments supporting the study of macromolecules using NMR, CD, dynamic light scattering, analytical ultracentrifugation, stopped-flow kinetics, isothermal titration calorimetry, microscale thermophoresis and mass spectrometry. Applicants should submit a curriculum vita and three letters of reference by July 10, 2017 to Diana Tomchick, Chair, Structural Biology Laboratory Search Committee, U.T. Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-8816. UT Southwestern is an Affirmative Action/Equal Opportunity Employer. Women, minorities, veterans and individuals with disabilities are encouraged to apply. For further inquiries, please contact: Diana Tomchick Department of Biophysics, Rm. ND10.214A UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas TX 75390-8816 Tel. +1 214 645 6383 Email: Diana.Tomchick(a)UTSouthwestern.edu<mailto:[email protected]> ? ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 Diana.Tomchick(a)UTSouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Amit D invited you to check out Dropbox
by Dropbox 20 May '17

20 May '17

Hi there, Amit D (amitd453(a)gmail.com) thinks you should use Dropbox! It’s a free and easy way to access and share your docs, photos, and videos with colleagues and friends—even if they don’t have Dropbox accounts. Accept invite[1] Get started through this email, and you’ll get an extra 500 MB added to your 2 GB of free space. Happy Dropboxing! [1]: https://www.dropbox.com/l/AADiCZMqlucm1Gb-DwLfoxb-Ub8mVCIREm0

1 0

pdb help
by jp d 19 May '17

19 May '17

hi, phenix version 1.11.1-2575 FEM has crashed a few times for me . i have tried using various parameters (resolution_factor=1./3, use_resolve=False) , but it will max out my RAM (24G) and get into swap space. It gets very memory intensive, i think thats why it crashed. Do you have any suggestions to try ? i previously had a similar problem with a pdb using conflicting chain assignments, but this pdb doesn't use chains thanks jpd

2 1

Electronic Laboratory Notebook
by Sebastiano Pasqualato 19 May '17

19 May '17

Dear all, another enquiry for the great community! We are considering the idea of moving to electronic laboratory notebooks rather than paper ones. Are you happily using one and would warmly suggest its implementation? Our department does not only deal with biochemical experiments, but performs a lot of genomics (big data analysis) and mouse genetics experiments, so experience of Notebooks used in departments that also have those activities would be a plus. We will consider free and paid softwares, if you have information on the costs that would be also very much appreciated! Thanks a lot, ciao Sebastiano -- 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

1 0

Associate Researcher Position at the University of Kansas Protein Structure Laboratory
by Lovell, Scott W 17 May '17

17 May '17

The Protein Structure Laboratory at the University of Kansas is seeking a full-time Associate Researcher to assist with various structural biology projects. For a full description and to apply, GO TO: https://employment.ku.edu/staff/8691BR Review of applications begins 5/30/17 Regards, Scott __________________________________ Scott Lovell Ph.D., Director Protein Structure Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 Email: swlovell(a)ku.edu<mailto:[email protected]> Website: https://psf.cobre.ku.edu/cores/psl/about Phone: 785-864-3772 __________________________________

1 0

kick maps
by jp d 12 May '17

12 May '17

hi, sorry if this is easily googleable, but i am not having any luck. how can i generate a kick map? thanks jpd

2 1

Error running ERRASER
by Eric Montemayor 12 May '17

12 May '17

Has anybody encountered this error when running ERRASER in Phenix? If so, any suggestions for how to fix this would be greatly appreciated! -------------------------------------------------------------------------- *TypeError : ('__init__() takes at least 3 arguments (1 given)', <class 'subprocess.CalledProcessError'>, ())Traceback (most recent call last): File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/App.py", line 784, in OnTimer self.run_manager.update(update_backgrounded=False) File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/ProcessControl.py", line 213, in update process.update() File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/phenix/wxGUI2/ProcessControl.py", line 136, in update self._process.update() File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/cctbx_project/libtbx/runtime_utils.py", line 306, in update (error, traceback_info) = easy_pickle.load(self.error_file) File "/opt/sbgrid/i386-mac/phenix/1.11.1-2575/phenix-1.11.1-2575/modules/cctbx_project/libtbx/easy_pickle.py", line 82, in load return cPickle.loads(_open(file_name, "rb").read())TypeError: ('__init__() takes at least 3 arguments (1 given)', <class 'subprocess.CalledProcessError'>, ())* -------------------------------------------------------------------------- -- Eric J. Montemayor, Ph.D. Associate Scientist University of Wisconsin-Madison 145 Biochemistry Laboratories 433 Babcock Drive Madison, WI 53706 512.784.5981 http://about.me/montemayor https://www.linkedin.com/in/ericmontemayor <https://www.linkedin.com/pub/eric-montemayor/63/121/98b>

2 2

ERRASER fails to run on ribosome model
by #AHMED TOFAYEL# 11 May '17

11 May '17

Dear PHENIX and ERRASER developers, While ERRASER is running fine (command line) when I use a small PDB file, it fails repeatedly on a complete ribosome model giving following error: Starting erraser Date: Tue May 9 17:53:20 2017 Directory: /home/tofayel/Desktop/test HOSTNAME: localhost.localdomain Log file will be /home/tofayel/Desktop/test/erraser.log Splitting output to /home/tofayel/Desktop/test/erraser.log Running ERRASER Rosetta app... ################################### Path to ERRASER: /usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER ERROR: Unique best command line context option match not found for -fixed_res. Possible matches include: -willmatch:fixed_res -stepwise:fixed_res -rna:farna:erraser:fixed_res Either specify namespace from command line; or in code, use add_relevant() to register option. Traceback (most recent call last): File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/erraser.py", line 14, in <module> erraser_run=phenix.erraser.erraser.erraser(args=sys.argv[1:]) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 349, in __init__ self.run(params,out=out) File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/erraser/erraser.py", line 459, in run erraser(option) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 92, in erraser full_struct_slice_and_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 662, in full_struct_slice_and_minimize erraser_minimize( minimize_option ) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_wrapper.py", line 488, in erraser_minimize subprocess_call(command, sys.stdout, sys.stderr) File "/usr/local/rosetta_src_2016.32.58837_bundle/tools/ERRASER/erraser_util.py", line 101, in subprocess_call subprocess.check_call(command, shell=True, stdout = out_channel, stderr = err_channel) File "/usr/local/phenix-1.11.1-2575/base/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/usr/local/rosetta_src_2016.32.58837_bundle/main/source/bin/erraser_minimizer.linuxgccrelease -database /usr/local/rosetta_src_2016.32.58837_bundle/main/database/ -s /home/tofayel/Desktop/test/test-model-coot-19_erraser_temp/minimize_0_full_minimize_temp/before_min_temp_rs.pdb -score:weights stepwise/rna/rna_hires_elec_dens_FCC2012 -score:rna_torsion_potential FCC2012_RNA11_based_new -rna::corrected_geo true -rna::rna_prot_erraser false -rna::vary_geometry true -constrain_P true -attempt_pyrimidine_flip false -rna:farna:erraser:skip_minimize false -chemical:enlarge_H_lj false -in:guarantee_no_DNA false -scale_d 100 -scale_theta 10 -stepwise:rna:o2prime_legacy_mode true -use_2prime_OH_potential false -fixed_res 78 79 100 101 102 106 107 108 109 110 115 116 -edensity:mapfile /home/tofayel/Desktop/test/test-map.ccp4 -edensity:mapreso 3.3 -edensity:realign no -graphics false -skip_connect_info true ' returned non-zero exit status 255 Please suggest some fixes. Thanks in advanced. Best regards, Tofayel

2 1

error when running the tutorials?
by Murpholino Peligro 10 May '17

10 May '17

[murphy@eva00 tut-phenix]$ phenix.run_example gene-5-mad Examples to be run: gene-5-mad Running PHENIX example: gene-5-mad Wed May 10 21:24:26 CDT 2017 Working directory: /home/murphy/X-Rays/tut-phenix/gene-5-mad Starting run now ... please wait a moment Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] Traceback (most recent call last): File "/home/murphy/X-Rays/phenix/phenix-dev-2747/build/../ modules/cctbx_project/site.py", line 48, in <module> import os ImportError: No module named os tutorial files look ok. ps running phenix dev2747 happens the same thing with p9-sad

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how to run Rosetta using phenix GUI interface on windows
by chen c 08 May '17

08 May '17

Hi, everyone, Can anybody tell how to run Rosetta using phenix GUI interface on windows system? Thank you so much! Best regards Chen -- Cheng Chen, Ph.D. Candidate Laboratory of Structural Biology Life Science Building,Tsinghua University Beijing 100084 China Tel:+86-10-62772291 Fax:+86-10-62773145 E-mail:[email protected] 北京市海淀区清华大学生命科学馆201-212室邮编：100084

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phenix real space refine & free R reflections
by Hillen, Hauke 05 May '17

05 May '17

Dear Phenix bb, I have a rather conceptual question regarding the treatment of free R flags in phenix.refine and phenix.real_space_refine. I am refining an xray structure using phenix.refine (but not using the real space refinement implemented there) and at some point decided to play a bit with the standalone program phenix.real_space_refine. In particular, I was interested in testing real space refinement against different maps (experimental map vs. model-phased). Being used to the excellent handling of free R flags in Phenix, I assumed giving phenix.real_space_refine the output MTZ of a previous phenix.refine run as a map would be safe to do. But I then saw the phenix.refine FAQ states the following: "Are R-free flagged reflections included in the maps used for real-space refinement? No, this is almost guaranteed to bias R-free; these reflections are removed internally prior to map calculation. However, the output maps will include these reflections unless you explicitly request otherwise.” While it makes sense to me that including the free reflections in the maps used for real space refinement will bias R-free, I wonder why the default behavior of phenix.refine is to output maps which include these reflections. I assume most users will use these output maps (for example via the OPEN IN COOT button in the GUI) to iteratively improve their model by local real space refinement in Coot. Conceptually, how is real space refinement performed by phenix.refine (where the free R reflections are not used to calculate the map to refine against) different from manual local real space refinement in Coot? Will the latter not also bias R-free when the default output maps from phenix.refine are used? Best, Hauke

3 4

Different stats with different number of macrocycles
by Patrick Loll 05 May '17

05 May '17

Hi, I have an odd observation. I am finishing a refinement at 2.5 Å, using the Phenix GUI. I performed a three-macrocycle refinement, and saw that the geometry (RMS bonds/angles) and R/Rfree all got better in the first macrocycle, and then worsened in the subsequent two macrocycles. OK, fine. So I repeated the refinement, except I performed only a single macrocycle (starting from the exact same input coordinates). However, the statistics after this one-macrocycle job did not match the stats seen after 1 macrocycle in the 3-macrocycle job (?!). This doesn’t make sense to me; if you’re starting from the exact same coordinates, shouldn’t the first macrocycle always wind up at the same place, regardless of whether or not the program goes on to do additional macrocycles of refinement? In case this isn’t clear: In the 3-macrocycle job, after the first macrocycle, RMS bonds/angles = 0.005 Å/0.9 deg, R/Rfree = 0.208/0.236 (by the end of the third macrocycle, these numbers have changed to 0.009 Å/1.41 deg and 0.212/0.244) At the end of the 1-macrocycle job, RMS bonds/angles = 0.008 Å/1.4 deg, R/Rfree = 0.209/0.240 This is Phenix version 1.11.1-2575-000. Any insights welcome. Cheers, 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 pat.loll(a)drexelmed.edu

5 8

Phenix Generate Table 1 Tool for twin-refinement statistics
by Xiao Lei 04 May '17

04 May '17

Dear All, I am using Windows Phenix Version 1.11.1. I'd like to generate table 1 for journal using Phenix "Generate Table 1 tool". In the input column, I input pdb model, data mtz, and data unmerged mtz, it gives me output statistics without twin refinement. But I'd like to show the results of twin refinement because I used Refmac5 to do twin refinement. Even I put the pdb from the output after twin refinement, the tool still gives me without twin refinement statistics. Thanks ahead for any input.

1 0

TLS refinement
by Reza Khayat 02 May '17

02 May '17

Hi, I'm having difficulty with performing TLS refinement on a highly symmetric system. The difference between the R_work and R_free increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The TLS tensors for some of the group are not sensible (if I understand the literature correctly) -there are some negative numbers for the T and L tensors (see below). The TLS groups were identified with phenix.find_tls_groups. Any suggestions would be appreciated. REMARK 3 SELECTION: chain 'A' and (resid 38 through 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.6459 -23.5648 -59.0695 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.2895 REMARK 3 T33: 0.0962 T12: 0.0829 REMARK 3 T13: 0.0473 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.0446 L22: 0.0120 REMARK 3 L33: 0.0096 L12: 0.0246 REMARK 3 L13: 0.0209 L23: 0.0106 REMARK 3 S TENSOR REMARK 3 S11: 0.0228 S12: -0.0268 S13: -0.0023 REMARK 3 S21: -0.0507 S22: 0.0526 S23: -0.0287 REMARK 3 S31: -0.0296 S32: -0.0137 S33: 0.0534? The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

2 1

starting model using phenix.map_to_model
by Chang Sun 01 May '17

01 May '17

Hi there, I am currently using the phenix.map_to_model for model building from a cryo EM electron density map. One thing I am wondering is whether the starting model should be aligned with the original map or the shifted map produced in the process? Because in my case, most of the starting model is not retained in the final "map_to_model.pdb". BTW, Dr Terwilliger, thanks for devoloping this wonderful tool! Thanks, Chang Postdoctoral Research Associate , Gennis Lab Department of Biochemistry, University of Illinois A306 CLSL 600 S. Goodwin Ave Urbana, IL 61801 Phone: 217-333-4939

1 0

FSC curve between experimental cryo EM map and model
by #AHMED TOFAYEL# 28 Apr '17

28 Apr '17

Dear all, If I want to calculate FSC curve between experimental cryo EM map and model, what is the correct procedure to do so? I will explain what I have tried so far. Although I have variable local resolution in my map, according to FSC=0.143 criterion I have a 4 Ang map (say 1.mrc), I have used 'molmap' command in Chimera to generate a simulated map at 4 Ang. Then I used "vop resample" to take care of the pixel and box values ( then saved as 2.mrc). Thereafter, I have used "e2proc3d.py 1.mrc fsc.txt --calcfsc=2.mrc and plotted the fsc.txt file to get the curve. I am not sure if I am on the right track. My pixel size is 1.28. Best regards, Tofayel

2 1

radiation damage-induced phasing (RIP) tutorial
by Murpholino Peligro 28 Apr '17

28 Apr '17

Hi lads... Do you know if there is a good tutorial for doing RIP somewhere on the internet? What programs can do RIP? -SHELX -AutoRickShaw -? Thanks

1 0

Can I use PHENIX "Find NCS" tool to verify space group ?
by Alex Lee 23 Apr '17

23 Apr '17

Hi All, I have a protein/dna dataset (3A resolution) with space group (SG) ambiguity, it could be P32 with two copies of molecules (one copy of molecule composed of protein homodimer with asymmetric dsDNA) in asymmetric unit (ASU) or P3221 with one copy of molecule in ASU. Both SG can give me MR solutions and after Refmac P32 Rfree is around 31% while P3221 Rfree is around 34% (without any twin refine at this stage). Density maps from both SG makes sense and they are similar by eye inspection. Because of partial twinning of the dataset (estimation twin fraction alpha around 0.22) , which confuse programs of assigning the correct SG. Pointless and Xtriage suggests P6222, which we are sure it's not correct (based on performance on both MR, Refmac and biology sense that dsDNA is asymmetric, and if P6222 is true then based on Mathew coef. there will be a monomer protein with single strand ssDNA in ASU). Zanuda suggests SG P32 in both cases (input experimental data P32 or P3221 along with refined model). However, Zanuda may not work well in twin case. In short, the problem now is to choose one SG from P32 or P3221. There is one suggestion that try SG P32, as there are two copies of molecules in ASU in P32 group, try find the NCS operator in P32 and check if this operator is close to crystallographic symmetry operator or not, if it is, then SG is P3221, if it's not, then SG is P32. I did a few rounds of search in Internet, I found Phenix "Find NCS tool" and input PDB of my refined structures from both P32 and P3221. For both test, Find NCS tool did find NCS operator but in the end of the log file I see the same results as below: This NCS object does not contain point group symmetry This NCS object does not contain helical symmetry. I am asking: 1. does "This NCS object does not contain point group symmetry" from Find NCS tool mean that NCS operator in my PDB is not crystallographic symmetry operator? 2. Is there a tool in Phenix which can find the NCS operator and check if the NCS operator is close to crystallographic symmetry operator or not? Thanks ahead.

2 1

Marching tomorrow?
by lbetts0508 . 21 Apr '17

21 Apr '17

Dear all, I am marching in DC tomorrow for continued support of our wonderful National Laboratories and funding that made resources like PHENIX possible. What a treasure these have been. Thank you for your support of structural biologists all these years and I hope for your continued success! Laurie Betts Chapel Hilll,NC

2 1

Cannot compile rosetta interface Centos 7 with 1.11.1
by ludovic Pecqueur 21 Apr '17

21 Apr '17

Dear Phenix developers, I installed the latest phenix version today (1.11.1-2575) on Centos 7.2 I have rosetta_2016.13.58602 When I try to compile the rosetta interface (after exporting PHENIX_ROSETTA_PATH), compilation fails (see end of message for errors). When I compile the rosetta interface using phenix 1.11-2567, compilation goes to completion without errors. If you have any idea of the change between the two versions leading to this issue. Thank you for your help, Ludovic. ######################## Error message: Substituting phenix.python into build shell scripts update_options.sh update_ResidueType_enum_files.sh /usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source ~> phenix.python scons.py bin mode=release extras=python -j 8 scons: Reading SConscript files ... Running versioning script ... fatal: Not a git repository (or any parent up to mount point /usr/local) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). Done. (0.0 seconds) file ./options.dox being updated file ./full-options-list.md being updated Number of option files updated: 2 Total 3657 options. Finished updating ResidueProperty code -- no changes needed Finished updating VariantType code -- no changes needed scons: done reading SConscript files. scons: Building targets ... g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/hybridization/CartesianSampler.cc In file included from src/protocols/hybridization/CartesianSampler.cc:17:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/protocols/cryst/cryst_movers.cc In file included from src/protocols/cryst/cryst_movers.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. gcc -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libsqlite3.so -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/dbio/sqlite3/sqlite3.os -L/usr/lib -L/usr/local/lib -Lexternal/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/external/release/linux/3.10/64/x86/gcc/4.8/python/libcifparse.so -Wl,-rpath=/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/rosetta_src_2016.13.58602_bundle/main/source/build/external/release/linux/3.10/64/x86/gcc/4.8/python -Wl,-rpath=\$ORIGIN -Wl,-rpath=\$ORIGIN/../lib -shared build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/BlockIO.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifDataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifExcept.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifFileReadDef.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DataInfo.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DicFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParserBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScannerBase.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Exceptions.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenCont.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/GenString.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ISTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ITTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_ptr_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/mapped_vector.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/ParentChild.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/RcsbPlatform.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/Serializer.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TableFile.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/TTable.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/CifScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICParser.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/DICScanner.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regcomp.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regerror.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regexec.os build/external/release/linux/3.10/64/x86/gcc/4.8/python/cifparse/regfree.os -Lexternal/lib -Lbuild/external/release/linux/3.10/64/x86/gcc/4.8/python -Lexternal -L/usr/lib -L/usr/local/lib -lpython2.7 -ldl -lpthread -lutil g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/PhenixInterface.cc In file included from src/core/scoring/cryst/PhenixInterface.cc:15:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. g++ -o build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os -c -std=c++98 -ffor-scope -isystem external/boost_1_55_0/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -pipe -Wall -Wextra -pedantic -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DPTR_BOOST -DNDEBUG -DWITH_PYTHON=1 -Isrc -Iexternal/include -Isrc/platform/linux/64/gcc/4.8 -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isrc/platform/linux -Iexternal/boost_1_55_0 -Iexternal -Iexternal/dbio -I/usr/include -I/usr/local/include -Iexternal/include/python2.7 src/core/scoring/cryst/XtalMLEnergy.cc In file included from src/core/scoring/cryst/XtalMLEnergy.cc:16:0: src/core/scoring/cryst/PhenixInterface.hh:18:20: fatal error: Python.h: No such file or directory #include "Python.h" ^ compilation terminated. scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/hybridization/CartesianSampler.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/protocols/cryst/cryst_movers.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/PhenixInterface.os] Error 1 scons: *** [build/src/release/linux/3.10/64/x86/gcc/4.8/python/core/scoring/cryst/XtalMLEnergy.os] Error 1 scons: building terminated because of errors.

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Generate a map showing local agreement between map and model
by #AHMED TOFAYEL# 17 Apr '17

17 Apr '17

Dear developers and users, Is it possible to generate a map to show local agreement between cryo-EM map and the model generated using the same map? If I am not wrong, the supplementary figure S5 had accomplished the job (using Chimera), but I don't understand how to generate a similar figure for my project. Is it possible to do with phenix? http://emboj.embopress.org/content/28/6/755 Best regards, Tofayel NTU Singapore

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UTMB Sealy Center for Structural Biology Symposium - May 6 - Register NOW
by Mark A. White 17 Apr '17

17 Apr '17

You and your colleagues are cordially invited to join us for the 22nd Annual Structural Biology Symposium to be held at Levin Hall on the University of Texas Medical Branch Campus on beautiful Galveston Island on Saturday, May 6, 2017. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: James Chou, Ph.D., Harvard Medical School Rachelle Gaudet, Ph.D., Harvard University Petr Leiman, Ph.D., Univ. of Texas Medical Branch Daniela Nicastro, Ph.D., Univ. of Texas Southwestern Medical Center Brian Shoichet, Ph.D., Univ. California San Francisco School of Pharmacy Kylie Walters, Ph.D., Center for Cancer Research, National Cancer Institute To register or for more information, visit http://scsb.utmb.edu/symposium register: http://scsb.utmb.edu/symposium/2017/registration.asp

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Understanding Biology through Structure, Santa Fe May 13-17
by Terwilliger, Thomas Charles 14 Apr '17

14 Apr '17

Hi Colleagues! I hope you can come to our symposium on Understanding Biology through Structure in Santa Fe this May 13-17! The Symposium will emphasize interactions between junior and senior researchers. We hope that this will present a special opportunity for junior researchers to present posters and meet senior scientists, for senior researchers to meet the next generation of structural biologists, and for all to discuss science in an informal setting. You can see the full program at https://conferences.newmexicoconsortium.org/conferences/ubts_17/program Understanding Biology through Structure Santa Fe, NM May 13-17 2017 Speakers Nucleic acid and protein-nucleic acid complexes Jamie Cate, University of California, Berkeley Eva Nogales, University of California, Berkeley Jody Puglisi, Stanford University Leemor Joshua-Tor, Cold Spring Harbor Laboratory Tom Steitz, Yale University Shigeyuki Yokoyama, RIKEN Structural Biology of Cell Signaling Axel Brunger, Stanford University Sharon Campbell, University of North Carolina Yvonne Jones, Oxford University Dorothee Kern, Brandeis University Cynthia Wolberger, Johns Hopkins University Hao Wu, Harvard University Disease and Drug Discovery Lesa Beamer, University of Missouri Tom Blundell, University of Cambridge Elizabeth Goldsmith, UT Southwestern Medical Center Lynn Howell, University of Toronto Michael Rossmann, Purdue University Erica Ollmann Saphire, Scripps Institute Natalie Strynadka, University of British Columbia Ian Wilson, Scripps Institute Crystallographic Methods Wladek Minor, University of Virginia Randy Read, University of Cambridge Jane Richardson, Duke University Tom Terwilliger, Los Alamos National Laboratory Isabel Uson, Institute of Molecular Biology, Barcelona Nadia Zatsepin, University of Arizona Membrane Protein Structures Susan Buchanon, National Institutes of Health Wayne Hendrickson, Columbia University Robert Stroud, University of California, San Francisco Nieng Yan, Tsinghua University Protein folding and Design David Baker, University of Washington Ken Dill, Stony Brook University David Eisenberg, University of California, Los Angeles Susan Marqusee, University of California, Berkeley Tobin Sosnick, University of Chicago Understanding Enzyme Function Catherine Drennan, Massachusetts Institute of Technology Andrzej Joachimiak, Argonne National Laboratory Ci Ji Lim, University of Colorado, Boulder Ilme Schlichting, Max Planck Institute for Medical Research All the best, Tom T ?

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Deadline approaching: 10th CCP4/APS Crystallographic School in the USA
by Sanishvili, Ruslan 13 Apr '17

13 Apr '17

Dear Colleagues, The deadline for application to the annual CCP4/APS school in macromolecular crystallography: “From data collection to structure refinement and beyond” is in less than a week - April 19. Please read the thread below for basic information on the school. For all details, please visit http://www.ccp4.ac.uk/schools/APS-2017/index.php With regards, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, February 01, 2017 2:54 PM To: phenixbb(a)phenix-online.org Subject: [phenixbb] 10th CCP4/APS Crystallographic School in the USA Dear Colleagues, We are pleased to announce the 10th annual CCP4 crystallographic school “>From data collection to structure refinement and beyond”, held at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Dates: June 19 through 26, 2017 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop: beamline training; data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors, respectively; and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting of the technical difficulties the participants face in their projects. We have had considerable success resolving these problems in past years, attested by resulting publications http://www.ccp4.ac.uk/schools/APS-school/publications.php Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 19. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2017/index.php Registration fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation, lodging and breakfast. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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8th workshop on Neutron Scattering Applications in Structural Biology
by Meilleur, Flora 13 Apr '17

13 Apr '17

Second announcement 8th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 5 - June 9, 2017 Detailed information can be found on the workshop web page: https://conference.sns.gov/event/66/ Application deadline: April 22, 2017 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome - however the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meilleurf(a)ornl.gov<mailto:[email protected]> before April 22, 2017. Flora Meilleur, Ph. D Associate Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747

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