- phenixbb - phenix-online.org

model statistics
by wtempel 17 Jan '18

17 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 12 Jan '18

12 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 09 Jan '18

09 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 09 Jan '18

09 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 08 Jan '18

08 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 03 Jan '18

03 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 06 Dec '17

06 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. 04 Dec '17

04 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 20 Nov '17

20 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 15 Nov '17

15 Nov '17

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Max_reasonble_bond_distance error in phene.resl.space.refine
by Rune Thomas Kidmose 15 Nov '17

15 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 15 Nov '17

15 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 13 Nov '17

13 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 09 Nov '17

09 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 08 Nov '17

08 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 07 Nov '17

07 Nov '17

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kicked map calculations
by Ursula Schulze-Gahmen 07 Nov '17

07 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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