- phenixbb - phenix-online.org

Local sharpening error
by Ricardo Righetto 19 Jan '18

19 Jan '18

Hi, I am trying to do local sharpening with phenix.auto_sharpen, with the following command: phenix.auto_sharpen map.mrc resolution=4.0 local_sharpening=True Then it runs the global sharpening first as expected, but when it gets to the local sharpening it crashes with the following error: Sorry: Please specify a sequence file with seq_file=myseq.seq Nowhere it says that I would need a .seq file in order to do local sharpening (global sharpening works fine). Any ideas? Thanks, -- Ricardo Diogo Righetto

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Autobuild in to "extra density"
by Tom Terwilliger 19 Jan '18

19 Jan '18

Hi Ben, I think you've done the hard part already by building a poly-ala model into your extra density! If you want to try and sequence it using the density, you can use phenix.replace_side_chains with the keyword "sequence_from_density=True" to do this. See: https://www.phenix-online.org/documentation/ reference/replace_side_chains.html To use autobuild with this, add an extra line to your sequence file with the sequence of the extra piece (separate it from the previous sequence with a blank line or a ">".) I would try rebuild_in_place=True to try and optimize the position of your extra chain. You can specify what residues to work on with something like: rebuild_chain_list=A rebuild_res_start_list=27 rebuild_res_end_list=35 This will rebuild chain A27 through A35. For density modification you might want to use a mask based on your model. For this you would say: mask_from_pdb=my_existing_pdb_file.pdb Let me know if that doesn't do it! All the best, Tom T Date: Tue, 9 Jan 2018 20:50:41 +0000 From: "Flath, Ben" <bef206(a)mail.usask.ca> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Autobuild in to "extra density" Message-ID: <52cba352941e48869fc9d5223a97ccaf(a)Mail06.usask.ca> Content-Type: text/plain; charset="us-ascii" Hi All I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31. My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of? Any help would be much appreciated. Regards Benjamin Flath, M.Sc. Research Assistant, Cygler Lab University of Saskatchewan Department of Biochemistry Room 3D40 HSCI Box 27, 107 Wiggins Road Saskatoon, SK S7N 5E5 Phone: 306 220-7355 email: benjamin.f(a)usask.ca<mailto:[email protected]> -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0033

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Fourier shell correlation (FSC) in cryo-EM refinement
by oleg＠quantumbioinc.com 18 Jan '18

18 Jan '18

I started to do some refinements of cryo-EM structures. But I could not find FSC (e.g. FSC average) quality metrics in the refinement log. Is it because of the real space refinement methodology or some features need to be activated? Please advise Thanks Oleg

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model statistics
by wtempel 18 Jan '18

18 Jan '18

Pre-1.13, the `model_statistics=True` option of PDBTOOLS produced a listing of average B-Factors, atom counts, etc. Is this functionality provided by another command in the current version of PHENIX? Many thanks. Wolfram Tempel

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keeping ligand rigid in phenix refine
by Vikram Dalal 13 Jan '18

13 Jan '18

Hi all, I want to keep my ligand positions rigids during phenix refine, so that its position wont affected after phenix refine. Thanks & Regards, VIKRAM DALAL Research Scholar

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"standard" monomer restraints
by wtempel 11 Jan '18

11 Jan '18

Hello, how/where (in the PHENIX installation tree?) can one look up target values (effective during restrained refinement in PHENIX) for specific bond lengths and angles of monomers like amino acids or nucleosides? Thanks. Wolfram Tempel

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Autobuild in to "extra density"
by Flath, Ben 10 Jan '18

10 Jan '18

Hi All I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31. My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of? Any help would be much appreciated. Regards Benjamin Flath, M.Sc. Research Assistant, Cygler Lab University of Saskatchewan Department of Biochemistry Room 3D40 HSCI Box 27, 107 Wiggins Road Saskatoon, SK S7N 5E5 Phone: 306 220-7355 email: benjamin.f(a)usask.ca<mailto:[email protected]>

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Phenix version 1.13 released
by Paul Adams 10 Jan '18

10 Jan '18

The Phenix developers are pleased to announce that version 1.13 of Phenix is now available (build 1.13-2998). Binary installers for Linux, Mac OSX, and Windows platforms are available at the download site: http://phenix-online.org/download/ Highlights for this version: - phenix.map_to_model - better symmetry support and improved runtime efficiency - phenix.structure_search - structural library and internal support for mmCIF - phenix.ligand_identification - limit ligand size for search - Phaser 2.8.1 - various bug fixes - Structure Comparison - more/improved validation information (ligands, waters, cis/trans peptides, HIS protonation) - GUI - automatic validation after phenix.real_space_refine; visual improvements in validation - Improved handling of model mmCIF input/output - New Phenix video tutorials - Internal bug fixes and performance improvements - NEW FEATURES - Phenix.map_to_model: - Allows cases where symmetry that is neither point-group nor helical is present - Allows splitting runs into many small independent steps - Set defaults for quick=True to run somewhat more quickly - GUI - Validation information added to phenix.real_space_refine results - phenix.real_space_refine GUI accepts input for reference models - Polygon stand-alone GUI deprecated; rolled into Comprehensive Validation GUI - Old Polygon jobs cannot be restored - Validation GUI - Stoplight colors (green/orange/red) added to validation summary - In rotamer outlier table, uncalculated chi angles now display blank instead of None - Validation table columns adjusted to reduce whitespace - Updated dependencies - Python 2.7.13 -> 2.7.14 - Boost 1.56 -> Boost 1.63 - Numpy 1.8.1 -> 1.8.2 - phenix.structure_search: - Updated to November 2017 RCSB non-redundant library (representatives of 100% sequence-identity clusters.) - Changed to mmcif-based coordinate handling internally. - phenix.ligand_identification: - Added search limit on ligand sizes (Non-H atoms) - Run LigandFit algorithm internally as default. - Phaser-2.8.1 - bugfixes - anisotropy correction of map coefficients after MR - detection of duplicate solutions - correct cell for PDB after refinement of cell for input data - packing places molecules near origin in compact arrangement - Structure Comparison - Updated to include favoured, allowed and outliers for validations tabs such as rotamers - Add featurs such as ligands information & locations; water locations; cis/trans peptides; and histidine protonation - General increase of robustness and flexibility - Greater flexibility for model/data input including directory tree travesal and user defined scripts - Restraints - Added better SF4 restraints - Added mechanism to improve SF4 linking - Various performance enhancements - Better handling of model mmCIF input/output - New Phenix video tutorials: - Cryo-EM tools in Phenix - overview - How to run MolProbity - step by step (web interface and Phenix GUI) - MolProbity: All atom contacts tutorial 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 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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How to change the FOBS/SIGMA_FOBS value in phenix.refine
by 齐建勋 09 Jan '18

09 Jan '18

Dear PhenixBB, Is there place to set the I/SIGMA_I or FOBS/SIGMA_FOBS values in phenix.refine? I found the default FOBS/SIGMA_FOBS threshold in phenix.refine is 1.35, which means any reflection lower than 1.35 will be excluded in the refinement process. This will generally result in a lower completeness range especially for the relatively weak datasets. When I uses the xray_data.remove_outliers=False, I got the error message "Sorry: Unknown command line parameter definition: remove_outliers = False", and my PHENIX version is phenix-1.12-2829, thanks. Regards Jianxun ******************************************************************* Dr. Jianxun Qi A321, Institute of Microbiology, Chinese Academy of Sciences No.1 West Beichen Road, Chaoyang District Beijing 100101, China Email: jxqi(a)im.ac.cn Tel : 86-10-64806182 *******************************************************************

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Install Problem Linux CentOs 5
by Whitley, Matthew J 04 Jan '18

04 Jan '18

Hello all, We are trying to install the new 1.13-2998 release of Phenix on 64 bit Linux CentOs 5 and have run into some problems. We are logged in as root, and we were able to unzip and untar the archive with no problem. However, when we run the install script, we immediately get the following errors: root@linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]# ./install Traceback (most recent call last): File "./bin/install.py", line 20, in ? from libtbx.auto_build import install_distribution File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 75, in ? from libtbx.auto_build import install_base_packages File "/usr/local/phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_base_packages.py", line 864 os.chmod(filename, 0o755) # set permissions to -rwxr-xr-x ^ SyntaxError: invalid syntax [root@linux7 phenix-installer-1.13-2998-intel-linux-2.6-x86_64-centos5]# Any idea as to what the source of the problem is and how to get around it? Thanks for your help. Matthew Whitley --- Matthew J. Whitley, Ph.D. Research Instructor Department of Pharmacology & Chemical Biology University of Pittsburgh School of Medicine

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target bond/angle RMS deviations from ideal
by wtempel 14 Dec '17

14 Dec '17

Hello all, the documentation <https://www.phenix-online.org/documentation/faqs/refine.html> states that This is somewhat controversial, but absolute upper limits for a well-refined protein structure at high resolution are typically 0.02 for RMS(bonds) and 2.0 for RMS(angles); usually they will be significantly lower. I understand that exceedingly high RMSDs from ideal could indicate overfitting. On the other hand, local deviations from ideal geometry may point to correctable modeling errors, and I am concerned that overly tight restraints may cause that diagnostic tool to become less sensitive, or local errors to be spread in to the model. For what bond and angle rms deviations from ideal do my colleagues on the BB aim and how have they arrived at those targets? Did my web search miss a relevant paper? Thank you in advance. Wolfram Tempel

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Announcing the release of the Detergent Belt Server
by vincent Chaptal 13 Dec '17

13 Dec '17

This message is especially directed towards the membrane proteins community. Dear everyone, we are very pleased to announce the release of the Detergent Belt Server -> http://detbelt.ibcp.fr Following our discovery of a method to quantify detergents around membrane proteins, we have build the detbelt server to allow for a simple _representation of the detergent belt around your protein of interest_. This representation is a simple approximation and grants a rapid estimation of the detergent belt, especially fitted to _biochemists_ to better understand what is going on in your test tube. (Details on the server and the publication of the detergent quantification method are available on the tutorial page). The server allows you to play with different detergents interactively by recomputing the belt in your web browser, which allows you to refine your biochemical hypothesis. The server allows you to add several detergents, each with different values, and will compute the volume associated with these detergents mixtures. It outputs different metrics making it easier to compare detergent-occupied volumes, and a PyMOL script to generate a publication quality image. For the moment, membrane protein pdb file should be pre-oriented using the PPM server procedure as it runs slow on the server; please visit the tutorial web page for more details (see "1"). We are working towards speeding up this process and making it all integrated in the near future. For testing purposes, I attach a pre-oriented pdb so that you can have an idea of the information you can obtain. Finally, we welcome any feedback to this alpha release; we welcome bug reports as well as creative feedback: if you think this tool has some potential for your research, please contact us and we will see what can be done. Wishing you good visualization All the best The DetBelt team -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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reference_xray_structure
by yamei yu 07 Dec '17

07 Dec '17

Dear all, I want to use “reference model” in a low resolution structure refinement. Do I need to set this parameter “reference_xray_structure”? What does “reference_xray_structure” stand for? Many thanks and best wishes ************************************************ Yamei Yu Associate Professor State Key Laboratory of Biotherapy／Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyuxtal(a)gmail.com ymyuxtal(a)163.com yamei_yu(a)scu.edu.cn

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Re: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Jeffrey, Philip D. 05 Dec '17

05 Dec '17

To put this in context: I originally wrote that page when phenix.refine used a |F|>0 cutoff in refinement. Given that I<0 often results in |F|=0 after the conversion the program threw out data for which we knew something (i.e. it was weak) albeit imprecisely. That was a self-evidently bad idea. However the defaults in phenix.refine have changed and as Ed Berry observes it does emulate CCP4's TRUNCATE now (in "truncate yes" mode, probably). I convert my data with CCP4's TRUNCATE or CTRUNCATE programs. For strong data I don't apply the French and Wilson intensity data remapping. For weak data I do - but only for refinement purposes, not for SAD/MAD phasing. My standard ploy is to use CAD to strip out Imean and SigImean from the MTZ file so that phenix.refine cannot attempt to "outsmart" me again. And by outsmart I really mean "usurp my intentions". I would suggest that everyone do the same - or at least test the difference. My known bias is to trust CCP4 programs more. Cheers Phil Jeffrey Princeton ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Xiao Lei [xiaoleiusc(a)gmail.com] Sent: Saturday, December 02, 2017 9:05 PM To: PHENIX user mailing list Subject: [phenixbb] Is it harmful to to use Imean SigImean in Phenix Refine by default? Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Is it possible to restrain Cartesian NCS for ligands?
by Edward A. Berry 04 Dec '17

04 Dec '17

Is it possible to restrain cartesian NCS for ligands in phenix.refine? I included a ligand in an paired ncs-group and it seems to be omitted from the listing of those groups in the log file. When I made an ncs_group including only ligands, it halted complaining of empty selection. Ed

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Is it harmful to to use Imean SigImean in Phenix Refine by default?
by Xiao Lei 04 Dec '17

04 Dec '17

Dear All, I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead." This may force rejecting weak data according to the post. The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 21 Nov '17

21 Nov '17

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission for the January 2018 issue is 20 December 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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Bug in 2.10.3 with scrolling
by Mark Saper 21 Nov '17

21 Nov '17

If one scrolls an alignment (not WRAP mode), the names of the sequences scroll but not the sequences with it. Using the scroll bar works correctly. Running 2.10.3 on MacOS 10.12.6 with Java version: 1.8.0_151. 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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Ligand library error in Phenix.Refine
by Gyanendra Kumar 17 Nov '17

17 Nov '17

Hi there, My Phenix.Refine run crashes because of non-availability of dictionary file for "ACP", a non-hydrolyzable ATP. Could this ligand be added to the next nightly build? Phenix.Refine suggested using "ReadySet", but that also failed. I sent the error reports to bugs(a)phenix-online.org, all emails bounced back. Refmac runs fine. Thanks! -Gyan -- Gyanendra Kumar, PhD Associate Scientist, St. Jude Children's Research Hospital, Department of Structural Biology, 262, Danny Thomas Place, MS-311 Memphis, TN 38105 Cell: 631-875-9189 https://www.linkedin.com/in/gyanendrakumar https://scholar.google.com/gyanendrakumar <https://scholar.google.com/citations?user=lnil0IQAAAAJ&hl=en> https://www.researchgate.net/profile/Gyanendra_Kumar3 http://stjude.academia.edu/GyanendraKumar -------------------------------------------------------

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(no subject)
by Rajendra Sharma 16 Nov '17

16 Nov '17

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Max_reasonble_bond_distance error in phene.resl.space.refine
by Rune Thomas Kidmose 16 Nov '17

16 Nov '17

I have been playing around with phenix.real.space.refine as part of a small pipeline I am making for EM structures. Testing various deposited EM structures and their corresponding maps, within my pipeline, I sometimes run in to the below error: RuntimeError: Bond distance > max_reasonable_bond_distance: 79.8663 > 50: Followed by a list of distances between, what I am assuming is, atom numbers and the actual distance. I can get past it simply by changing the max_reasonable_bond_distance for the run to, in this case, 80. But I tend to see, that the final results gets significantly worse when I use this bypass. This is based on very similar models going through the pipeline, where the ones which yields the error, scores much worse when using the above mentioned bypass, compared to the models that showed no max_reasonable_distance_error. So I was wondering: A: What does "max reasonable bond distance" actual mean? B: Any ide what I can do, to avoid running into this bond distance problem? I know the latter is asking a lot, as I have not disclosed any of the details surrounding how the error arose etc. but if such info is needed, I would prefer to do so off list and then return with the solution on list, if possible. Maybe I was hoping for a setting that ignores the outliers, without changing the max value. But that all depends on, what the setting actual is, which I dont know Cheers Ruki

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Twin refinement problem
by Leonid Sazanov 16 Nov '17

16 Nov '17

Dear all, there seems to be a problem with twin refinement of some of our datasets, and I wanted to see if that is something specific to our data or if anybody else has seen it. These crystals have been reproduced many times and are always twinned in P21 space group with twin operator: -h,-k,h+l and twin fraction in the range 0.45 - 0.49. Data always refines fine in Refmac and in many cases in Phenix as well, giving similar twin fraction in both programs. However, with some datasets (at 3.4-3.6 A resolution) in Phenix there is a problem: refinement of twin fraction is unstable and jumps each macro-cycle between about 0.40 (wrong?, giving high R-factors) and 0.47 or so (true?, giving much lower R-factors). This can be clearly seen from log file extract: cycle stage r-work r-free twin_fraction 0 : 0.3002 0.3084 1_adp: 0.2511 0.2701 0.49 2_adp: 0.2724 0.2837 0.42 3_adp: 0.2296 0.2465 0.47 4_adp: 0.2464 0.2587 0.40 5_adp: 0.2230 0.2420 0.47 6_adp: 0.2393 0.2554 0.40 7_adp: 0.2225 0.2423 0.47 8_adp: 0.2416 0.2590 0.40 9_adp: 0.2184 0.2376 0.47 10_adp: 0.2380 0.2556 0.40 end: 0.2393 0.2568 0.39 ------------------------------------------- The same dataset refines with stable twin fraction = 0.48 in refmac. When Phenix accepts higher twin_fraction with its lower R-factors, it does cycles 0 and 1 of twin fraction refinement once, while when it fails to update and falls back to low twin_fraction, it does this twice, as shown below. Updates OK: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2383 0.2381 0.2565 n_refl.: 191608 twin_fraction=0.40 re-set all scales: r(all,work,free)=0.2926 0.2926 0.2950 n_refl.: 191608 twin_fraction=0.40 cycle 0: update twin fraction: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2910 0.2933 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2473 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 update scales twin start: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 reset f_part, k_(total,mask): r(all,work,free)=0.2910 0.2911 0.2934 n_refl.: 191608 twin_fraction=0.47 bulk-solvent and scaling: r(all,work,free)=0.2249 0.2246 0.2472 n_refl.: 191608 twin_fraction=0.47 r_work=0.2246 r_free=0.2472 twin_fraction=0.47 twin_law=-H,-K,H+L ============================ Set refinement target ============================ Falls back: =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2216 0.2214 0.2408 n_refl.: 191608 twin_fraction=0.47 re-set all scales: r(all,work,free)=0.2855 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.47 cycle 0: update twin fraction: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2854 0.2855 0.2848 n_refl.: 191608 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2186 0.2184 0.2377 n_refl.: 191608 twin_fraction=0.48 start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 re-set all scales: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 cycle 0: update twin fraction: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 update scales twin start: r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 reset f_part, k_(total,mask): r(all,work,free)=0.2783 0.2782 0.2848 n_refl.: 191509 twin_fraction=0.48 bulk-solvent and scaling: r(all,work,free)=0.2330 0.2329 0.2486 n_refl.: 191509 twin_fraction=0.48 cycle 1: update twin fraction: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 update scales twin start: r(all,work,free)=0.2306 0.2305 0.2458 n_refl.: 191509 twin_fraction=0.40 reset f_part, k_(total,mask): r(all,work,free)=0.2781 0.2780 0.2846 n_refl.: 191509 twin_fraction=0.40 bulk-solvent and scaling: r(all,work,free)=0.2295 0.2293 0.2439 n_refl.: 191509 twin_fraction=0.40 r_work=0.2374 r_free=0.2522 twin_fraction=0.40 twin_law=-H,-K,H+L ============================ Set refinement target ============================ With some other datasets Phenix just gets stuck at apparently in-correctly low twin fraction - each cycle it tries to update to 0.47-0.48 (and R factors are better in this case) but then it always falls back to 0.36-0.40 again. So I wonder if anybody else has seen this with their data? Many thanks for any info! Leonid -- Prof. Leonid Sazanov IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Postdoctoral research position
by Demetres D. Leonidas 15 Nov '17

15 Nov '17

Postdoctoral research position: molecular biologist/bioinformatician A 2-year Post-Doctoral position is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated and creative scientist with a track record of successful research. A good bioinformatics background is strongly desired. The ideal candidate should be able to analyze raw sequencing data, perform genome assembly and annotation and have a good understanding of comparative and functional genomics. At the same time, he/she should be able to design and perform experiments in support of the bioinformatics analyses. Candidates should have a PhD and should have training in one or more of the following disciplines: bioinformatics, molecular biology, biochemistry, cell biology, and genome-wide technologies. Familiarity with insect rearing is desirable but not essential. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmathiop(a)bio.uth.gr. Research position: MSc Bioinformatician A 2-year position for an MSc Bioinformatician is available immediately in the Laboratory of Molecular Biology and Genomics in the Department of Biochemistry and Biotechnology of the University of Thessaly, located in the city of Larissa. The selected candidate will work in the framework of a national Research Infrastructure program on Synthetic Biology. Research in the Laboratory of Molecular Biology and Genomics focuses on various aspects of insect olfaction, reproduction and evolution, aiming at the development of new approaches for control of insects of agricultural or medical importance. We are seeking a highly motivated individual with a BSc in Biology or related science and an MSc in Bioinformatics. The successful candidate will be involved in raw sequencing data analysis, genome assembly and annotation and comparative and functional genomics studies. His/her research could also lead to a PhD. Curriculum Vitae, a brief letter describing interests and prior experience and names of three references should be sent to: kmathiop(a)bio.uth.gr. -- ----------------------------------------------- Dr. Demetres D. Leonidas Professor of Biochemistry Department of Biochemistry & Biotechnology University of Thessaly Biopolis 41500 Larissa, Greece --------------------------------------------- Tel. +302410 565278 Tel. +302410 565297 (Lab) Fax. +302410 565290 E-mail: ddleonidas(a)bio.uth.gr http://www.bio.uth.gr ORCID ID orcid.org/0000-0002-3874-2523 ----------------------------------------------- --- Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus. https://www.avast.com/antivirus

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bgroup refinement of ZN ions
by Ursula Schulze-Gahmen 14 Nov '17

14 Nov '17

I have 2 Zn ions which are defined as HETATM, in my structure. I am using tls and bgroup refinement for the whole structure. It seems like the Zn ions are treated as one group. They always have the same B-value. I would like to refine the B-value of the ZN ions separately, but refine the rest of the structure with bgroup refinement. Is that possible? How would I do this? 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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mmtbx.prepare_pdb_deposition sequence file
by Ursula Schulze-Gahmen 10 Nov '17

10 Nov '17

I have problems running 'mmtbx.prepare_pdb_deposition' on the cif file created in phenix. I think the problem may be the sequence file. The coordinates are from a complex of 4 proteins plus an RNA. I created a text file with 5 chains, each chain sequence in one letter code. I am getting the following error code when I try to run the program: Traceback (most recent call last): File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 99, in <module> run(sys.argv[1:]) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/build/../modules/cctbx_project/mmtbx/command_line/prepare_pdb_deposition.py", line 69, in run alignment_params=params) File "/home/programs/x86_64-linux/phenix/1.12-2829/phenix-1.12-2829/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 1052, in as_cif_block_with_sequence assert len(chain.residue_groups) + chain.n_missing_start + chain.n_missing_end == len(sequence) There seems to be something wrong with chain N, but I am not sure what. Is it ok to have a longer sequence in the sequence file than in the coordinates? 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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chain and residue ID in phenix.erraser
by Ursula Schulze-Gahmen 09 Nov '17

09 Nov '17

I am trying to run phenix.erraser, but I am not able to define the single residue for rebuilding correctly. I am getting error messaheg: Please make sure that you include both the chain ID and residue number, for example 'A15'. I want to rebuild nucleotide G32 in chain N, and defined the residue as N32. That is not correct. What would be the correct syntax for this case? 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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Question about writing cif files at the last round of refinement
by Boaz Shaanan 08 Nov '17

08 Nov '17

3 5

kicked map calculations
by Ursula Schulze-Gahmen 08 Nov '17

08 Nov '17

I am trying to calculate kicked maps in the phenix GUI, but I don't get the option, nit in the mtz files, and not in the CCP4 map option. Could that have something to do with this error message I am getting when starting Phenix: Gtk-Message: Failed to load module "canberra-gtk-module" Gtk-Message: Failed to load module "pk-gtk-module" Or are there any settings I need to change? 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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data fill in in phenix refine?
by Ursula Schulze-Gahmen 26 Oct '17

26 Oct '17

I have data from a crystal with anisotropic diffraction. After scaling and merging using the webserver staraniso, I would like to refine using phenix refine. Could you tell me if phenixrefine will try to fill in the missing reflections that were removed in the staraniso procedure? If so, is there a a way to prevent this fill in? Following is the warning message for the Staraniso server: We are grateful to Andrew Leslie (MRC-LMB) for identifying a potentially undesirable 'feature' of CCP4/REFMAC (and possibly other refinement software), namely the 'fill-in' of unobserved data with *DF*calc which makes it effectively *incompatible* with the MTZ file output by STARANISO. Our advice is therefore to use *BUSTER <http://www.globalphasing.com/buster>* for refinement using the downloaded MTZ file, unless the user can find a way to disable that feature in the alternative software. In general, any treatment of STARANISO's output data that adds missing reflections out to the resolution limit may result in a very high proportion of unobserved data compared with data that have had a cut-off applied according to an isotropic criterion. Where missing reflections have been added in this way the user should take care to verify that any applications used to process the data subsequently can handle it correctly. 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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Announcing the release of CryoFIT
by Nigel Moriarty 24 Oct '17

24 Oct '17

Dear colleagues, We are excited to announce the release of CryoFIT, a program for fitting atomistic models to cryo-EM maps. The current version is designed for fitting lower resolution maps but this does not preclude use with higher resolution maps. The CryoFIT modules is built on Gromacs and accessible through Phenix (https://www.phenix-online.org/documentation/reference/ cryo_fit.html), currently via GitHub. It supports both the Phenix GUI and the command line. CryoFIT is based on the algorithm in Kirmiziatltin, et al., Methods of Enzymology 2015 (https://doi.org/10.1016/bs.mie.2015.02.011). This is an alpha version. Please send any feature requests and bug reports to Doo Nam Kim (doonam(a)lanl.gov). Happy Modeling! 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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Email addresses for bug reports
by Billy Poon 24 Oct '17

24 Oct '17

Hi everyone, We've been receiving bug reports with incorrect or dummy email addresses (e.g. "go away.com"). While we read through all of these bug reports, we cannot respond to them without correct email address. Before submitting a bug report from the Phenix GUI, please make sure that the email address is correct. Alternatively, bug reports can be sent to bugs(a)phenix-online.org. 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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Re: [phenixbb] [cctbxbb] Update to allsvn script?
by Billy Poon 21 Oct '17

21 Oct '17

Hi all, Is anyone still using "allsvn" from the phenix_regression repository? If not, we'll just delete it next Friday (10/27) since it's hopelessly out of date. The functionality has been superseded by bootstrap.py. 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 On Thu, Oct 19, 2017 at 11:22 PM, <Graeme.Winter(a)diamond.ac.uk> wrote: > Folks, > > phenix_regression/allsvn assumes if you are using git that you are using > git/svn > > These days probably not true ;o) > > Viz: > > > cd cctbx_project; git svn rebase > > Unable to determine upstream SVN information from working tree history > > > ccp4io: At revision 160. > > ccp4io_adaptbx: At revision 142. > > cd dials; git svn rebase > > Unable to determine upstream SVN information from working tree history > > someone on phenix-land want to have a look at this? Obviously not a > blocker but is untidy! > > Thanks Graeme > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb >

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Job opening: Postdoctoral Fellow in Structural Biology and Drug Discovery
by Schonbrunn, Ernst 20 Oct '17

20 Oct '17

Dear Madam/Sir, Please post the following open postdoctoral position on your job-board. Thank you, Ernst Schonbrunn ----------------------------------------------------------------------------------------------- Postdoctoral Fellow in Structural Biology and Drug Discovery Location: Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612 Department: Drug Discovery Department Job Details: Moffitt Cancer Center is internationally recognized for our focus on personalized cancer care and translational research. The mission of Moffitt is clear, focused, and fully stated in nine words, "To contribute to the prevention and cure of cancer." With a tradition of excellence that began with the first patient admission in 1986, dedicated Moffitt physicians, scientists, and staff members have remained committed to excellence in an atmosphere characterized by kindness, caring, and hope. The Schönbrunn lab studies the structure-function relationship of medicinally relevant proteins along with the discovery and development of novel small molecule inhibitors as therapeutics. We are involved in multiple projects working in team with medicinal chemists, biologists and clinicians on the targeting of proteins involved in cell signaling and epigenetic events. For an overview of our research approach and current projects please visit our web site at labpages2.moffitt.org/schonbrunn/<http://labpages2.moffitt.org/schonbrunn/>. Position Highlights: · We seek highly motivated postdoctoral researchers to work on inter-disciplinary projects towards the characterization and inhibitor development of diverse kinases and bromodomain-containing proteins. * The position provides exciting opportunities for biochemical, structural and cell-based studies of various drug-target interactions and rational drug design. The Ideal Candidate: · The ideal candidate has a Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field and expertise in protein crystallography and biochemistry as demonstrated by publications in internationally recognized scientific journals. * Additional experience in cell biology is preferred. Responsibilities: · Candidates must be enthusiastic and dedicated to science with excellent organizational skills and effective at working independently, while also collaborating and assisting the team in its collective research goals. * Attention to detail and ability to work on multiple projects is required. * Excellent verbal and written communication skills are required. Credentials and Qualifications: * Ph.D. degree in Biochemistry, Biology, Chemistry, Physics or related field. A competitive salary and benefits package will be offered to the successful candidate. Interested applicants should send a single PDF file that includes a current CV with recent publications, a personal statement of scientific interests and goals (2-page maximum) and contact information for three references to Dr. Ernst Schönbrunn at Ernst.Schonbrunn(a)moffitt.org<mailto:[email protected]> Equal Employment Opportunity Moffitt Cancer Center is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, or protected veteran or disabled status. We seek candidates whose skills, and personal and professional experience, have prepared them to contribute to our commitment to diversity and excellence. [MOFFITT_2c_RGB for signature] Ernst Schönbrunn, PhD Associate Professor Moffitt Cancer Center 12902 Magnolia Drive, Tampa, FL 33612 | tel: 813-745-4703 | email: ernst.schonbrunn(a)moffitt.org Please consider the environment before printing this email. This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you.

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Install Phenix 2926 on Linux Fail
by Xiao Lei 19 Oct '17

19 Oct '17

Dear All, I was trying to install Phenix 2926 on Ubuntu Mate, after type sudo ./install I got the following fail message: ========================================================= Phenix Installation version: dev-2926 machine type: intel-linux-2.6-x86_64 OS version: 4.4.0-97-generic destination: /usr/local/phenix-dev-2926 # of processors: 4 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 275, in <module> installer(sys.argv[1:]).install() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 197, in install self.install_from_binary() File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 319, in install_from_binary self.reconfigure(log=log) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/install_distribution.py", line 379, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/linchenlab/Downloads/phenix-installer-dev-2926-intel-linux-2.6-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-dev-2926/base/bin/python /usr/local/phenix-dev-2926/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-dev-2926/build --command_version_suffix dev-2926 phenix phaser solve_resolve labelit dials xia2 iota prime' failed with exit code 1 What I need to do to fix this?

2 2

SHELX sites to use in Phenix.
by Mahmudul Hasan 18 Oct '17

18 Oct '17

Dear All, I am trying to solve a structure using Phenix with very low anomalous signal. After several trials it seems like the signal from Manganese is not enough to solve this protein structure. Reading information that SHELX is good in finding sites from low molecular weight molecules (e.g. S, etc.), I tried the online version of SHELX in CCP4 to find the sites. Now I would like use these sites found by SHELX to see if that help to solve the structure. My question is, what is the best way to include extra sites besides the program Autosol find itself? Your valuable suggestions will help me a lot to get going with my structure solution effort. Best wishes, Mahmudul Lund Sweden

2 1

Model_vs_data speed
by Eric Williams 17 Oct '17

17 Oct '17

I'm having a devil of a time getting model_vs_data to run in a timely fashion. Running the latest stable Linux build on Ubuntu 14.04 takes on the order of 3 minutes per structure. That wouldn't be so bad if I weren't trying to run it on every entry in the PDB. Is it just a limitation of Python? SFCheck, which I think is written mostly in FORTRAN, runs in a few seconds. Any help anyone could offer would be appreciated. Thanks. :) Eric

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Re: [phenixbb] Small change in molprobity report on output pdb between dev-2873 and dev-2919?
by Christopher Williams 10 Oct '17

10 Oct '17

I'll take a look. Thanks for noticing! -Christopher Williams ---Richardson Lab On Mon, Oct 9, 2017 at 12:44 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: > Hi Boaz, > > I had to disable it because it required re-calculation of all other > Molprobity metrics twice, which it time waste. > > @developers: Can someone from Richardson Lab fix this? > > Pavel > > > > On 10/9/17 09:35, Boaz Shaanan wrote: > > Hi, > > I noticed a small change in output pdb between these two versions in the > molprobity report (these are two different runs, so ignore the numerical > values)t: > > *dev-2919:* > > REMARK 3 REMARK 3 > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 3.13 > RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 3.24 % > REMARK 3 FAVORED : 96.30 % > > *dev-2873:* > > REMARK 3 MOLPROBITY STATISTICS. > REMARK 3 ALL-ATOM CLASHSCORE : 2.56 > REMARK 3 MOLPROBITY SCORE : 1.24 This line is missing from the > newer version > REMARK 3 RAMACHANDRAN PLOT: > REMARK 3 OUTLIERS : 0.46 % > REMARK 3 ALLOWED : 2.78 % > REMARK 3 FAVORED : 96.76 % > > I am just wondering whether this change is intentional. > > Cheers, > > Boaz > > > > > > > > > > *Boaz Shaanan, Ph.D. Dept. of Life > Sciences Ben-Gurion University of the > Negev Beer-Sheva > 84105 > Israel > E-mail: > bshaanan(a)bgu.ac.il <bshaanan(a)bgu.ac.il> Phone: 972-8-647-2220 Skype: > boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * > > > > > > > > _______________________________________________ > phenixbb mailing [email protected]://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > >

1 0

Rosetta installation
by Daniele de Sanctis 08 Oct '17

08 Oct '17

Hi all I have some trouble installing rosetta. I followed the instruction as in https://www.phenix-online.org/documentation/reference/rosetta_install.html and everything went ok up to % rosetta.build_phenix_interface nproc=n but then % rosetta.run_tests fails with Rosetta command-line arguments: -parser:protocol /buffer/desancti/xtal/rosetta_src_2016.32.58837_bundle/main/source/src/apps/public/crystal_refinement/low_resolution_refine.xml -s 1yjp_rosetta_in.pdb -mtzfile 1yjp_rosetta_data.mtz -run:preserve_header -crystal_refine -parser:script_vars symmdef=1yjp_rosetta.symm -parser:script_vars bfactstrat=individual -parser:script_vars map_type=Auto -score:weights talaris2013_cart -nstruct 1 Generating 2 models on 1 processors... DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) Traceback (most recent call last): File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/buffer/desancti/xtal/phenix/phenix-1.12-2829/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Any idea? thanks Daniele

2 1

Running Phaser with a already placed solution from a previous job
by vincent Chaptal 05 Oct '17

05 Oct '17

Dear everyone, this sounds trivial but I somehow can't make it work so I would appreciate any pointer. I have placed a component using phaser and would like to expand my search using this already placed component as partial solution. I open the full-featured interface of phaser in the GUI and select the box "Use partial solution from previous job" and select the job (nothing seems to happen there). I define my ensembles with ensemble_1 as "fixed partial solution" and ensemble_2 the one to search for. I then get the error message that "ense_1 from previous job is not specified on the current ensemble tab". Using the info button I see that "It is best to do this by modifying the configuration of the GUI from the previous Phaser run instead of starting from scratch, because the stored solutions do not contain the definitions of the search ensembles" but I don't understand what is asked for me to do here. When I restore the previous job, I can't see how I can start a new search from there. Any help would be greatly appreciated. Thanks Vincent I'm using phenix 1.12-2829. -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug Resistance and Membrane Proteins Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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map model correlations in real_space_refine
by Daniel Larsson 04 Oct '17

04 Oct '17

In version 1.12, what does the new map correlation numbers CC_mask, CC_volume and CC_peak in the log mean? How do they relate to the old "Map CC (whole unit cell)" and "Map CC (around atoms)" values (which in my opinion are more intuitive/descriptive and very useful numbers and I don't understand why they are no longer written to the log). Regards, Daniel

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help with phenix.ligand_identification
by Edward A. Berry 28 Sep '17

28 Sep '17

I'm having some problems using ligand_identification. I would like to restrict the search to a specific density peak, even if it is not the highest unmodeled peak or the highest Fo-Fc peak in the map. I tried using options: search_center="67.5 18.3 11.8" or ligand_near_res=S2063, Will the search be restricted to that region, or if a particuar ligand doesn't fit that blob, will it search through the rest of the map? If it is restricted, in what radius? Is this radius affected by the "search_dist" or "local_search" parameters? and local_search = True is default? Is there a threshold level for density level, below which building a ligand in a blob will not be attempted? I've tried with both search_center= and ligand_near_res=, and something gets built far away from that site. But there were errors, so I may have something wrong: phenix.ligand_identification mtz_in=sqr2803or13_031.mtz input_labels="2FOFCWT PH2FOFCWT" \ model=sqr2803or13_031.pdb ligand_near_res=S2063 nproc=2 After preparing the ligand library, then: Running LigandFit process 1... Number of atoms in ligand suc.pdb is 23 Running job sequence 1, ligand 2, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1... Evaluating all ligands in ligand-lib now...and placing fittedligand ### in resolve_ligand_###.pdb Number of atoms in ligand 2pe.pdb is 28 Running job sequence 0, ligand 1, in /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0... Process Process-2: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_1/LigandFit_run_1_/TEMP0' Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1382, in RunLigandFit shutil.rmtree(ligandfit_dir) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 247, in rmtree rmtree(fullname, ignore_errors, onerror) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 256, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 254, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: '/tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2/Temp_0/LigandFit_run_1_/TEMP0' Evaluating LigandFit results ... The run continues, but it does not test any more ligands after those first two but goes on to evaluate the results. With nproc = 1, only 1 ligand gets tested. In all cases the first ligand in the library (2PE.pdb) is evaluated as the best. It is placed in density, but density that has already been built out with (and looks more like) a string of water molecules. And this is far from the selected residue or coordinates specified. The directory that raised the error when attempting to be deleted does eventually get removed: after the run there is no TEMP_N in the parent directory. Any suggestions would be welcome. Ed P.S. - running with .eff file: ['--show_defaults'] ligand_identification { mtz_in = sqr2803or13_031.mtz mtz_type = *F diffmap model = sqr2803or13_031.pdb ncpu = 1 n_indiv_tries_min = 30 n_indiv_tries_max = 300 n_group_search = 4 search_dist = 10 local_search = True search_center = "67.5 18.3 11.8" # ligand_near_res = S2063 verbose = False debug = False use_ligandfit = True search_mode = *default LigandFit temp_dir = Auto dry_run = False # number_of_ligands = 1 cc_min = 0.75 open_in_coot = False non_bonded = True keep_all_files = False # cif_def_file_list = real_space_target_weight = 10 # job_title = None ligandfit { } } gives: [['2pe.pdb', 'suc.pdb', . . . 'upl.pdb']] /tb/sb/usr20c/berry/ref/sqrdep/sqr2803dep2/phenix2 ******************************************************************************* Sorry, the protein model file None does not seem to exist? ******************************************************************************* Running LigandFit process 0... Process Process-1: Traceback (most recent call last): File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/sw/lnx/phenix-1.12-2829/build/../modules/phenix/phenix/command_line/ligand_identification.py", line 1122, in RunLigandFit shutil.copyfile(mtz_in,data_local) File "/sw/lnx/phenix-1.12-2829/base/lib/python2.7/shutil.py", line 82, in copyfile with open(src, 'rb') as fsrc: IOError: [Errno 2] No such file or directory: 'None' Evaluating LigandFit results ... Lig_seq Placed/total cc_all cc cc_adj score Code HBscore Cannot find overall_ligand_scores.log0. This could mean that none of that (sub)set of ligand fitted well. None of the ligand fit the difference desity well enough. Please try the following -- 1) if you input a custom library, try to use the default library (no extra keywords needed), or 2) if you used the default library already, ususlly this means that the density is too small (> 6 atome or more is needed.) Exiting ...... No good ligand found.

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"Headless" install
by Jared Sampson 26 Sep '17

26 Sep '17

Hi all - Is it possible to download and install the latest Phenix release to a node on a computing cluster (i.e. without a screen and therefore web browser)? I've tried pasting the latest download links into `curl` and `wget` commands but get zero-size files as a result. Thanks, Jared

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Deadline reminder: XChem fragment screening at Diamond (and iNEXT) - SUNDAY 1st OCTOBER
by Frank von Delft 23 Sep '17

23 Sep '17

Dear Protein Crystallographers and Drug Discoverers A reminder that we are again inviting proposals for performing crystal-based fragment screening at Diamond's XChem facility at beamline I04-1, for the next allocation period (April 2018 to Sept 2018). *The deadline for proposals is NEXT SUNDAY 1st OCTOBER 5PM.* *Details of how to submit at this page <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening/Applying-for-Fragm…>. * Full details of the facility are available here <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html>. It supports the full crystal-to-structure experiment, and since opening for users in 2015, it has hosted over 50 users from academia and industry, with over 65 experiments (>50k crystals) consistently yielding credible, high quality fragment hits. With the right crystals, it'll keep you busy for less than a few weeks; and you get lots of support and advice. The calls are heavily oversubscribed, so please pay close attention to the instructions and guidelines. Access for EU users is funded via iNEXT <http://www.inext-eu.org/> (but only if you follow the instructions!); however we welcome all international proposals. -- Prof Frank von Delft Associate Professor Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 Visiting Professor Department of Biochemistry University of Johannesburg South Africa

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refine error message
by Jiemin Zhao 23 Sep '17

23 Sep '17

Hi， I got an error message when I try to refine a molecular replacement result. It says "number of nonbonded interaction distances<0.001:10. Please inspect the out put above(or in the log window) and correct the input model file." Could you help me with this problem? The error happens when I add Mg to pdb file. Thanks! Best regards, Jiemin

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Weird occupancy values in HySS
by Dominic Gilzer 22 Sep '17

22 Sep '17

Dear everybody, I am using Phenix HySS to solve the substructure of an iodine soak. I tried several high resolution cut-offs and a varying amount of heavy atoms to search for, but consistently get occupancies of > 1.0. Has anyone noticed such values for occupancies before, and by chance knows how or why these occur? Best regards, Dominic

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refine error message
by Jiemin Zhao 19 Sep '17

19 Sep '17

Hi, I got an error message when I try to refine a molecular replacement result. It says Fatal problems interpreting model file: Number of atoms with unknown nonbonding energy type symbols: 18 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply-cif-modification and apply-cif-link parameter definitions if necessary. Could you help me with this problem? Thanks! Best regards, Jiemin

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Academic position in cryoEM at The University of York
by Jon Agirre 15 Sep '17

15 Sep '17

The Department of Chemistry at The University of York is seeking to make an appointment of a Lecturer/Senior Lecturer/Reader/Professor in the area of Cryo Electron Microscopy, the position being based in the world-renowned York Structural Biology Laboratory within the Department. The Department has been awarded >£2M by the Wellcome Trust and Wolfson Foundation to invest in state-of-the-art equipment and a bespoke building to house a modern 200 kV cryo-electron microscope, supported by significant investment from the University and a private donor. We are now seeking to appoint a high-calibre researcher in cryo-electron microscopy, with a clear vision to lead their own programme of excellent research within YSBL <https://www.york.ac.uk/chemistry/research/ysbl/>. Your research will complement the X-ray crystallography and NMR techniques currently used in the YSBL, and will bridge the gap between X-ray work and the optical microscopy in the Biology Technology Facility. The role is available at any level and we welcome interest from talented academics with an impressive research profile appropriate to the level of application and a collegiate approach to their work. You will be a dynamic research leader with a consistent track record in the application of cryo-electron microscopy to challenging biochemical/biological problems. We welcome applications from researchers with an interest in diverse areas of structural and cell biology, with particular interest in those working on mammalian systems. The Department of Chemistry is one of the UK's leading Chemistry departments and is renowned internationally for its research, having performed exceptionally strongly in the recent Nature Index 2017 Innovation Table <https://www.york.ac.uk/chemistry/news/deptnews/nature-index-2017-innovation…>. Combined with a commitment to high-quality teaching and outstanding student satisfaction, it is recognised consistently for its family-friendly policies and is proud of its Athena SWAN Gold Award. *Key requirements:* (viewed relative to the level of post applied for – see candidate briefs for more details) - PhD in Chemical, Biochemical or Physical Sciences - Specialist knowledge in cryo electron microscopy - Ability to undertake high-quality research and publish in leading, peer-reviewed journals - Ability to define, lead, manage and attract funds for research, operating across disciplinary boundaries - Experience of and commitment to teaching and learning at undergraduate level. - Demonstrable capacity for creative thinking and planning - Substantial recent publication record in leading peer-reviewed journal - Evidence of national and/or international collaboration *Why York?* We are a dynamic, research-intensive university and have experienced significant growth over the past ten years, securing national and international recognition for our academic excellence. Our attractive, landscaped campus has seen significant development which will continue as the University continues to develop. Chemistry is a multidisciplinary department with an international reputation for excellence in research and teaching. www.york.ac.uk/chemistry *Salary will be commensurate with experience and grade* Lecturer: £38,832 to £47,722 Senior Lecturer: £49,149 to £56,950 Reader: £49,149 - £60,410 Professorial: current minimum £62,585 *To apply* Informal enquiries may be directed to Head of Department Professor Duncan Bruce (chem-hod(a)york.ac.uk; +44 (0)1904 322500) or the Academic Group Leader in YSBL Professor Tony Wilkinson (tony.wilkinson(a)york.ac.uk; +44 (0)1904 328261) Link: https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885&p_we… *Closing date:* 9 October 2017 *Interviews will be held in York on:* 29 November 2017 -- Dr Jon Agirre Royal Society University Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8270 Twitter: @alwaysonthejazz

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Macromolecular Crystallography workshop in South America
by Felipe 13 Sep '17

13 Sep '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). This Workshop will cover all aspects of the macromolecular structure determination process using X ray crystallography: starting from data processing, through phasing and refinement to structure completion and analysis. Integrative methods are also being included. In particular, this year an introduction to cryo-electron microscopy has been added to the program. http://pasteur.uy/mx2017 <http://pasteur.uy/mx2017> Dates: November 13 - 23, 2017 Confirmed speakers and tutors: Alejandro Buschiazzo, Montevideo, Uruguay Grzegorz Chojnowski, Hamburg, Germany Paul Emsley, Cambridge, UK Richard Garrat, São Carlos, Brazil James Holton, San Francisco/Berkeley/Palo Alto, USA 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 <http://pasteur.uy/mx2017> 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 <mailto:[email protected]> Looking forward to welcoming you in Montevideo! Felipe Trajtenberg, PhD Laboratory of Molecular & Structural Microbiology Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 143 Fax: +598 25224185 http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular… <http://pasteur.uy/en/laboratorios-eng/microbiologia-estructural-y-molecular…>

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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 12 Sep '17

12 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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