- phenixbb - phenix-online.org

on Phenix10
by Smith Lee 28 Sep '15

28 Sep '15

Dear All, With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling. Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A? Smith

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Re: [phenixbb] Rosetta refine compilation issue Centos 7 (ludovic Pecqueur)
by Kay Diederichs 28 Sep '15

28 Sep '15

just a wild guess - could it be that, according to http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Phenix#Installa… the Phenix installer requires (on Fedora and RHEL) the openssl-devel and libXt-devel to be installed on the system ? HTH, Kay Am 28.09.15 um 03:24 schrieb phenixbb-request(a)phenix-online.org: > 8. Re: Rosetta refine compilation issue Centos 7 (ludovic Pecqueur) > > Message: 7 > Date: Wed, 23 Sep 2015 14:09:08 -0700 > From: Paul Adams <pdadams(a)lbl.gov> > To: ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7 > Message-ID: <68387823-8DAE-4C7F-84DF-5D79D36A3AD0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Ludovic, > > the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? > > Cheers, > Paul > >> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> wrote: >> >> Dear Developers, >> >> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) >> >> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: >> >> [XXX@...]$ rosetta.build_phenix_interface nproc=6 >> False >> scons: Reading SConscript files ... >> Running versioning script ... Done. (0.1 seconds) >> Could not find platform independent libraries <prefix> >> Could not find platform dependent libraries <exec_prefix> >> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >> ImportError: No module named site >> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: >> main() >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: >> SConscript("SConscript", "build") >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: >> return method(*args, **kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: >> return _SConscript(self.fs, *files, **subst_kw) >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: >> exec _file_ in call_stack[-1].globals >> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: >> subprocess.check_call(["./update_options.sh"]) >> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: >> raise CalledProcessError(retcode, cmd). >> >> If you have any idea of what could cause the problem, I would welcome any suggestions. >> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. >> >> Thank you very much for your time and help. >> >> Kind regards, >> >> Ludovic. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >

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Rosetta refine compilation issue Centos 7
by ludovic Pecqueur 24 Sep '15

24 Sep '15

Dear Developers, I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: [XXX@...]$ rosetta.build_phenix_interface nproc=6 False scons: Reading SConscript files ... Running versioning script ... Done. (0.1 seconds) Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: main() File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: SConscript("SConscript", "build") File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: return method(*args, **kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: return _SConscript(self.fs, *files, **subst_kw) File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: exec _file_ in call_stack[-1].globals File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: subprocess.check_call(["./update_options.sh"]) File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: raise CalledProcessError(retcode, cmd). If you have any idea of what could cause the problem, I would welcome any suggestions. I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. Thank you very much for your time and help. Kind regards, Ludovic.

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a question on phenix refine
by Smith Liu 23 Sep '15

23 Sep '15

Dear All, If my protein is rather large, and I have the mtz file of the whole protein, when I do phenix.refine of a single domain PDB of the whole protein against the whole protein mtz, after several cycles of phenix.refine the domain will not fit in the map at all (or even the domain moves far away from its initial position in map which it fits best), perhaps because the phenix.refine has made the domain to seek suitable fit in the map. Is any possibility at the whole process of phenix.refine we keep the domain relatively surround the map position where it fit best, so that phenix.refine will really do the refine in this situation? Best regards. Smith

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ADP restraints under TLS+individual ADP
by Tristan Croll 23 Sep '15

23 Sep '15

Hi, When taking a structure I refined in Phenix (using a TLS + individual ADP model) into a different refinement package, a colleague noted a host of warnings related to mismatched B-factors between the sulfur atoms in disulfide bonds. If I understand correctly, this arises due to Phenix falling back to a Ulocal only ADP restraints scheme and, in particular, the choice to set adp_restraints.iso.sphere_radius = 2.0. The length of a disulfide bond being 2.05A, this means that as long as the geometry is correct the B-factors of the two sulfurs are never restrained to each other under these conditions. Cheers, Tristan Tristan Croll Lecturer Faculty of Health School of Biomedical Sciences Institute of Health and Biomedical Engineering Queensland University of Technology 60 Musk Ave Kelvin Grove QLD 4059 Australia +61 7 3138 6443 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

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labelit distl_minimum_number_spots_for_indexing
by Christian Roth 22 Sep '15

22 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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Alternative conformations in Coot
by Nigel Moriarty 21 Sep '15

21 Sep '15

Folks A recent article by Pavel Afonine in the Computational Crystallography Newsletter highlighted the flexible interface for alternative locations in Phenix. You can read it here: http://phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 It recently came to my attention that some users who have an example of the Number 5 were having trouble viewing their models in Coot. After communicating with Paul Emsley, it turns out that you need a recent version of Coot (I ungraded from 0.8 to 0.8.2) and add the line allow_duplicate_sequence_numbers() to your ~/.coot.py file. You can test this using PDB 1ejg. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division 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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5'-phosphate group CIF files
by jens j birktoft 21 Sep '15

21 Sep '15

Hi everyone I need some suggestions for a CIF file for a 5'-phosphate moiety that is part of the nucleotide (CYT in this case) located at the start of a DNA strand (5' end) to be used in refinement in both PHENIX and COOT. All suggestions are appreciated. Cheers Jens -- +++++++++++++++++++++++++++++++++++++++++++++++++++ Jens J. Birktoft Structural DNA Nanotechnology New York University e-mail: birktoft(a)nyu.edu <jens.knold(a)gmail.com>; Phone: 212-749-5057 very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025 +++++++++++++++++++++++++++++++++++++++++++++++++++

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why does "phenix generate table 1 for journal" plot stats different from those of XSCALE for example?
by Almudena Ponce Salvatierra 21 Sep '15

21 Sep '15

Hi everyone, I am trying to find out why phenix outputs differnt stats for the high resolution shell than XSCALE does. Anybody has observed this earlier? Best, Almu -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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3rd Annual Conference on the Biological Applications of X-ray Free Electron Lasers - BioXFEL
by Edward Snell 16 Sep '15

16 Sep '15

Dear all, This is not a directly related Phenix topic but the meeting may be of interest to Phenix users. Please note that the announcement also appeared on the CCP4 bulletin board with some incorrect spellings of names. I apologize to those concerned - my fault completely with travel, a high resolution laptop screen, and discovering I now need glasses to read at that resolution all to blame. The 3rd Annual Biological Applications of X-ray Free Electron Lasers (BioXFEL) meeting will be held at the Intercontinental Hotel in San Juan, Puerto Rico, from Jan 13th to 15th 2016. The conference is supported as part of the National Science Foundations BioXFEL Science and Technology Center, a consortium of eight US institutions headed by Ed Lattman and John Spence. The conference will focus on new and developing methods and biological results from biological XFEL research. The last day will cover hybridized developments capturing the growing interplay between XFEL and synchrotron sources. Confirmed speakers include Henry Chapman, Vadim Cherezov, Guillermo Calero, Marco Cammarata, Bob Fischetti, Helen Ginn, Heinz Graafsma, Abbas Ourmazd, Ilme Schlichting, Joerg Standfuss, and Rachel Woldeyes. Many others along with the preliminary agenda are to be announced shortly. The meeting will include education opportunities for post-doctoral and graduate students and an education and diversity talk by Cathy Drennan. A poster session will be held and a selection of abstracts submitted will be selected to be presented orally. The previous meeting of the series attracted over 150 international attendees with the talks, schedule, and environment stimulating much discussion and resulting in new collaborations. A diverse mixture of investigators from academic, industry and national laboratories will be present along with post-doctoral and graduate students. Anyone with an interest in this rapidly moving field is invited to attend. The registration fee is $300 (or $200 for students) with registration and details at https://www.bioxfel.org/events/details/64. Poster abstracts (with a preference for giving a talk if selected) should follow the format described on the webpage and be submitted by email to euppington(a)hwi.buffalo.edu. While the registration deadline is November 15th, the poster deadline is later, December 15th. However, talks will be selected from posters submitted from now until the registration deadline, until the presentation slots are filled. If you know of others who may not read the CCP4 board, please pass this information along. Come join us for a scientifically stimulating conference in a productive setting. Sincerely, Edward Snell and George Phillips (BioXFEL 2016 chairs) Edward Snell Ph.D. CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, SUNY Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esnell(a)hwi.buffalo.edu Heisenberg was probably here!

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