- phenixbb - phenix-online.org

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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