November 2015 - phenixbb - phenix-online.org

Berkeley Server Downtime
by Paul Adams 05 Nov '15

05 Nov '15

Dear Colleagues, as part of routine maintenance at our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) The servers will be shutdown at 5pm Pacific time on Friday November 6th. Services should resume by the evening of Sunday November 8th at the latest. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience. Cheers, Paul -- Paul Adams Interim 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 80, Room 247 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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Modifying restraints for a single glutamate
by Eric Johnson 05 Nov '15

05 Nov '15

Is it possible to modify the restraints for single glutamic acid residue that forms an ester bond with a heme? Formation of the ester bond should lengthen the C - O bond length. Normal restraints distort the geometry of the covalent adduct. Thanks, Eric Johnson

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Installation problem
by Ricardo Padua 04 Nov '15

04 Nov '15

Hi all, I have the error below when trying to install Phenix in Centos6 running in a virtual machine (VMware workstation 12) in Win7 Enterprise. I've searched for this error in ccp4bb, phenixbb and google but nothing came out. Can anyone enlighten me? Best ========================================================================== Phenix Installation version: 1.10.1-2155 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-573.el6.x86_64 destination: /usr/local/phenix-1.10.1-2155 # of processors: 8 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/rpadua/.local/share/Trash/files/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos6/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 '/usr/local/phenix-1.10.1-2155/base/bin/python /usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code 127 Ricardo

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Formylmethionine
by mohamed noor 01 Nov '15

01 Nov '15

Dear all I am refining my model (1.8 A) where there is an excess density even after fitting the N-terminal Met. From Edman degradation data, the Met is actually an FME. However, only the density in one chain allows me to confidently place FME, and not for the other chain. The first chain also has a good enough density for me to be able to build all the residues in the protein except the last two at the C-terminus. So, do I model FME for both chains? Thanks. Mohamed

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