- phenixbb - phenix-online.org

Update: Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 15 Feb '16

15 Feb '16

Sorry, my previous email was incomplete. My structure has negative density in the center of some disulfides (the magnitude of this effect vary between different monomers in the ASU). I'd like to refine the structure in an "artificial reduced form", where cysteines involved in disulfides are treated in reduced form, but repulsions originating from neighboring sulfur atoms are turned-off, to monitor distances (I expect that SG atoms remain close to 2 A), guided only by data. Thank you, Ezequiel

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ensemble refinement
by George Kontopidis 15 Feb '16

15 Feb '16

Does ensemble refinement run on Phenix version 1.10.1-2155 (for windows) If yes can it run from GUI or only using command line? George

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REASONS UNKNOWN
by Almudena Ponce Salvatierra 15 Feb '16

15 Feb '16

-- 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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Re: [phenixbb] Arg, Glu, etc. naming conventions
by Mark A Saper 15 Feb '16

15 Feb '16

Apparently a torsion angle of –180° is considered very different from 0° because of the NH1.NH2 names. And the phenix convention is now different from coot. Mark _______________________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, U-M Medical School New location: Room 3220B, MSRB III | saper(a)umich.edu | +1 (734) 764-3353 On Feb 14, 2016, at 4:07 PM, Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> wrote: > Dear Mark, > I think Oleg is in the process of writing a little routine to fix problems in pdbs with regard to order of atoms in residues and such. Maybe fixing naming conventions could/will be included. > Cheers, > Eckhard > > > Am 14.02.2016 um 19:37 schrieb Mark A Saper: >> Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. >> -Mark >> _________________________________ >> Mark A. Saper, Ph.D. >> Associate Professor of Biological Chemistry, University of Michigan >> Ann Arbor MI 48109-1055 U.S.A. >> saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > -- > Prof. Dr. Eckhard Hofmann <eckhard.hofmann(a)bph.ruhr-uni-bochum.de> > Ruhr-Uni Bochum > AG Proteinkristallographie, LS Biophysik, ND04/318 > 44780 Bochum > Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762 > ORCID: 0000-0003-4874-372X

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Arg, Glu, etc. naming conventions
by Mark A Saper 14 Feb '16

14 Feb '16

Phenix 1.10.1 is flagging several of my Arg residues with bad dihedral angles. Phenix is much more strict about NH1, NH2 naming conventions then 6 months ago. Can these be fixed with PDB Tools? How? Many thanks in advance. -Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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Check for radiation-induced reduction of a disulfide bond
by Ezequiel Noguera 13 Feb '16

13 Feb '16

I'm working with one protein, crystallized in oxidized form, which exhibits negative density in the Fo-Fc map at the center of the disulfide bond. As a test of radiation-induced reduction during data collection, I'd like to do a trial refinement described in a previous work from literature, where SG sulfurs of involved cysteines were refined without van der Waals interactions to monitor distances of these atoms. How can I do this calculation in Phenix? Thanks in advance

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Using PyMOL-1.8 with PHENIX-dev-2306
by acyang 12 Feb '16

12 Feb '16

Hi everyone I've installed pymol and phenix on my scientific linux7.1 workstation. I can launch pymol via the launching script($PYMOL_HOME/pymol) normally. But when I launched pymol in phenix GUI, I got some error as followed: ********************************************************************************************************************************* Traceback (most recent call last): File "/opt/PyMOL/modules/pymol/__init__.py", line 71, in <module> import pymol File "/opt/PyMOL/modules/pymol/__init__.py", line 521, in <module> import pymol._cmd ImportError: /opt/PyMOL/modules/pymol/_cmd.so: undefined symbol: PyUnicodeUCS4_SetDefaultEncoding ********************************************************************************************************************************* After STFW*, *I knew the problem is about unicode variant (UCS2, UCS4). I also checked the configuration of two python. For /bin/python (adopted by pymol) >>> import sys>>> print sys.maxunicode1114111 And for $PHENIX_HOME/base/bin/python (adopted by phenix) >>> import sys >>> print sys.maxunicode 65535 My question is : How do I add the flag --enable-unicode=ucs4 in configuring Python-2.7.8_cci. I'd appreciate if any reply on this. acyang

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reattach jobs
by andre.stiel 12 Feb '16

12 Feb '16

Hi, how do I reattach a job to a project in the GUI. Say I took the GUI to prepare a commands file (.eff) and save it. Then I run the actual refine from the command line on another computer using the save commands file. After the job is done, how do I get the job back in the GUI. I do not find something to „load“ or „reattach“ a job. Thanks. André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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phenix install error on linux
by Min Zheng 11 Feb '16

11 Feb '16

Dear All, I am installing phenix, and get the following error: ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 3.11.10-29-default destination: /home/m/m_zhen01/phenix-1.10.1-2155 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/nfsexp/homes/m_zhen01/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-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 '/home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python /home/m/m_zhen01/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/m/m_zhen01/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 1 m_zhen01@LIBRA:~/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5> /home/m/m_zhen01/phenix-1.10.1-2155/base/bin/python Traceback (most recent call last): File "/usr/lib64/python2.7/site.py", line 564, in <module> main() File "/usr/lib64/python2.7/site.py", line 546, in main known_paths = addusersitepackages(known_paths) File "/usr/lib64/python2.7/site.py", line 276, in addusersitepackages user_site = getusersitepackages(kind) File "/usr/lib64/python2.7/site.py", line 244, in getusersitepackages user_base = getuserbase() # this will also set USER_BASE File "/usr/lib64/python2.7/site.py", line 230, in getuserbase from sysconfig import get_config_var File "/usr/lib64/python2.7/sysconfig.py", line 10, in <module> 'stdlib': '{base}/'+sys.lib+'/python{py_version_short}', AttributeError: 'module' object has no attribute 'lib' Thanks in advance, Min

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Refinement differences?
by Mark A Saper 11 Feb '16

11 Feb '16

Hi, I used Phenix, build 2037 to refine a a new structure. I reran the refinement (with the identical parameters) in build 2155 (v1.10.1) and obtained different statistics and slightly worse geometry. Any idea why? In 2037: start final --------------------------------------- R-work: 0.2488 0.2244 R-free: 0.3003 0.2851 RMS(angles): 1.67 0.80 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.2% (Goal: < 0.2%) Ramachandran favored: 94.5% (Goal: > 98%) Rotamer outliers: 8.7% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 3.14 Overall score: 2.19 2155 start final --------------------------------------- R-work: 0.2488 0.2331 R-free: 0.3003 0.2856 RMS(angles): 1.77 0.72 RMS(bonds): 0.020 0.004 Ramachandran outliers: 1.4% (Goal: < 0.2%) Ramachandran favored: 93.4% (Goal: > 98%) Rotamer outliers: 9.4% (Goal: 1%) C-beta outliers: 0 (Goal: 0) Clashscore: 4.10 Overall score: 2.36 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry, University of Michigan Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323

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