- phenixbb - phenix-online.org

ERRASER Updates
by Caleb Geniesse 05 Nov '15

05 Nov '15

Hi all, My name is Caleb and I am a research programmer in the Das lab who has taken over the maintenance of ERRASER. ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta and Phenix. While benchmarking the current state of ERRASER, I uncovered some discrepancies in the clash scores and outliers of the resulting models (compared to the original benchmark in Chou FC et al., 2012). Accordingly, I've made some updates to the ERRASER code within Rosetta addressing these issues. *To avoid possible inaccuracies introduced by these bugs,* *all PHENIX-ERRASER users should download/install a weekly build of Rosetta 2015.35 (released Sept. 24, 2015) or later.* For more extensive PHENIX-ERRASER documentation and installation notes, please see: https://www.phenix-online.org/documentation/reference/erraser.html. Please let me know if you have any questions! All the best, Caleb Geniesse

2 3

Berkeley Server Downtime
by Paul Adams 04 Nov '15

04 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 ] --

1 0

Modifying restraints for a single glutamate
by Eric Johnson 04 Nov '15

04 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

2 1

Installation problem
by Ricardo Padua 03 Nov '15

03 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

2 1

Formylmethionine
by mohamed noor 31 Oct '15

31 Oct '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

1 0

a question on rotamer restraints
by Smith Lee 31 Oct '15

31 Oct '15

Dear All, When I run phenix.real_space_refine, in the rotamer restraints step I meet the following error message: RuntimeError: rotatable bond atoms CG1-CD (as defined by tardy-tree): no match in rotamer-info.tor_ids Will you please let me know how to overcome this error? Best regards. Smith

4 4

CaBLAM validate - alternative output?
by Oliver Clarke 28 Oct '15

28 Oct '15

Hi all, I really like the idea of CaBLAM validate for model validation at low resolution based on the CA and backbone geometry, but the output is a little limiting - either text or kinemage right now. Would it be possible to create an output format that can easily be visualized (and turned into figures) in chimera, pymol or coot? Maybe a modified version of the input pdb with the CA/peptide outlier status mapped to the B-factor and occupancy columns? Cheers, Oliver.

1 0

Restraining/constraining partial occupancy waters
by David Briggs 27 Oct '15

27 Oct '15

Hi PhenixBB. I have a very minor problem with partial occupancy waters moving out of density during refinement I have 2 structures, one apo structure (~1.3Å), one ligand bound (~1.5Å). The ligand binding site contains a Calcium ion. In the apo form there are 2 waters co-ordinating this Calcium. In the ligand bound form, these waters are replaced by oxygen atoms within the ligand. However, the ligand is only at 0.5 Occupancy as part of the ligand lies on a crystallographic two-fold axis. The ligand itself refines well with occupancy fixed at 0.5, and the Bs are sensible. In the 50% of the molecules which don't co-ordinate ligand, two waters must co-ordinate the calcium ion, and in keeping with this, we see that the electron density around these positions is greater than would be expected for the 50% occupancy ligand. So I added 2 0.5 occupancy waters to the model at these positions. However, when I run phenix.refine (refining XYZ, real space, occupancy, and individual Bs (isotropic for the ligand & waters - for the protein I use anisotropic Bs) these two 'ghost waters' move out of the electron density and their Bs increase massively. *My questions are:* Is there any way to restrain these waters to their apo positions? Is this the correct approach? I had initially thought that reference model restraints might be useful here, but if I understand correctly, reference model restraints cannot be applied to waters - Is this correct? If I cannot restrain the waters to the apo positions, would I be justified in fixing (constraining) them? This seems a little extreme and I am loath to do it, but given the isomorphous apo structure, I do have evidence that in the absence of ligand waters do take up these positions. Can anyone help? Cheers, Dave [image: David Briggs on about.me] David Briggs about.me/david_briggs <http://about.me/david_briggs>

2 1

2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, March 30-April 2 2016
by Cathy Lawson 24 Oct '15

24 Oct '15

Dear Crystallography List Members, I'm forwarding info about this upcoming conference on image analysis in 3D cryoEM on behalf of the organizers. [Also, while I have your attention, a reminder to participate in the ongoing EMDataBank map and model challenges, see http://challenges.emdatabank.org.] <http://challenges.emdatabank.org.]> > We are pleased to announce the 2nd International Conference on Image Analysis in Three-dimensional Cryo-EM, to be held at Granlibakken Conference Center, Lake Tahoe, California from March 30 to April 2, 2016 (http://ncmi.bcm.edu/cryoemsoftware-2016). The 2016 Symposium builds on our very successful previous meeting on the same theme in 2014. > The goal of the Symposium is to discuss state of the art image analysis approaches to tackle challenging biological problems and to identify current limitations and remaining problems in the field as currently practiced. The goal will be for developers in this area, both established as well as students/postdocs to discuss the detailed algorithms and methodologies in this field in greater technical detail than is possible at more general meetings like the GRC. The central premise is that gaining a comprehensive and quantitative understanding of highly sophisticated machines, complexes, and organelles of the cell requires the active, timely and coordinated development of complementary image analysis and data mining algorithm and approaches. We have recruited an outstanding panel of speakers (current agenda provided in the web site). > > > Sessions: > > * Handling Compositional and Conformational Variability > > * High Resolution Subtomogram Averaging and Related Techniques > > * High Resolution Single Particle Analysis > > * Resolution Assessment, Model and Map Validation > > * Data Storage Roundtable > > * Poster Talks > > All session will focus on interactive discussions with plenty of time for questions. We will also have a poster session, and selected posters will be invited to give short-format talks. The early registration deadline for this workshop ends in Jan 2016. Registration details can be found at http://ncmi.bcm.edu/cryoem-software-2016. > > > Dorit Hanein, CHAIR & Steven Ludtke, Co-CHAIR > > ORGANIZING COMMITTEE > > Wah Chiu, Ed Egelman, Ben Hankamer, Masahide Kikkawa, David Mastronade, Pawel Penczek, Henning Stahlberg, Fei Sun, Niels Volkmann >

1 0

Raw data.....
by Jrh 24 Oct '15

24 Oct '15

Good morning Tim, Overnight thoughts: Another aspect that seems to me to be accelerating now is the use of the diffuse scattering in MX structure AND dynamics analysis. There are several really nice papers in the last year. I post this on the Phenixbb because the drive forward on this is linked to Phenix. My point obviously is that this involves the whole diffraction pattern. I recognise that raw diffraction data measured for 'conventional crystal structure analysis', to use a term, may not be ideal but nevertheless these papers show that analysis is developing and so, at the Beamline, if diffuse scattering is evident it seems to me not so burdensome to add a data sweep with stronger exposures and a smaller beam (ie to minimising obscuring the diffuse by the Bragg). Also, just to mention, to add to my last message to you, I could mention specifically the very important initiative taken by Wladek Minor at Virginia within the US Big Data new funding. He already has a portal to 2800 raw data sets. At Utrecht Loes Kroon Batenburg and Toine Schreurs have shown what can be done with personal weblinks to raw data these last three years. And of course the US Structural Genomics centres pioneered much of this too. Greetings, John Emeritus Prof John R Helliwell DSc_Physics FInstP FRSC FRSB Fellow of the ACA Emeritus Member of the British Biochemical Society School of Chemistry, University of Manchester, M13 9PL, UK.

1 0