- phenixbb - phenix-online.org

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

2 2

Fourier shell correlation (FSC) in cryo-EM refinement
by oleg＠quantumbioinc.com 19 Jan '18

19 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

1 0

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

2 1

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

2 1

"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

4 7

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]>

1 0

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 ] --

1 0

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 *******************************************************************

4 5

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

2 1

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

4 3