May 2018 - phenixbb - phenix-online.org

Anisotropy with TLS
by Eugene Osipov 31 May '18

31 May '18

Hi, everyone, Can someone shed a light on B-factor refinement in PHENIX.refine. I am refining the structure with 2.5 A resolution, with individual B-factors and automatically defined TLS groups. Despite isotropic refinement of B-factors I still see ANISOU entries for atoms. I figured out that these ANISOU lines appear only after TLS refinement. So the question is how these ANISOU values are calculated? -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osipov(a)gmail.com

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Berkeley Server Downtown (5/29 - 5/31)
by Billy Poon 30 May '18

30 May '18

Dear all, On Tuesday, May 29, our servers will be shut down starting at 5:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Thursday (5/31) at the latest. This will affect, - 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/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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postdoc crystallographer job offer; International Institute in Warsaw, 15th Jun
by Błażej Bagiński 30 May '18

30 May '18

Dear All, Bujnicki Lab (Laboratory if Bioinformatics and Protein Engineering, located in the International Institute of Molecular and Cell Biology in Warsaw) is looking for an experienced (post-doc level) crystallographer/structural biologist, with an interest in combining various experimental and computational methods for structure determination of RNAs and RNA-protein complexes. Our group is involved in theoretical and experimental research on nucleic acids and proteins. The current focus is on RNA sequence-structure-function relationships (in particular 3D modeling), RNA-protein complexes, and enzymes acting on RNA. The Institute have in-house crystallographic and computing facilities and is located in the Ochota campus, surrounded by Polish Academy of Science's institutes and University of Warsaw's departments of biology/chemistry/physics/medicine/mathematics interests. Please find the full job offer in the attachment, as well as in the link below. The deadline is on 15th of June 2018. http://genesilico.pl/employment/#5 The webpage of our group can be found here; http://genesilico.pl/ as well as more information about the Institute: https://www.iimcb.gov.pl/en/ For more information and questions, please contact this address: Bujnicki, Janusz: iamb(a)genesilico.pl Kind regards, Błażej Bagiński

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d99 resolution measure availability?
by Oliver Clarke 27 May '18

27 May '18

Hi, I think the “d99” criterion described in this preprint (https://www.biorxiv.org/content/early/2018/03/14/279844) looks like a really interesting FSC-independent way to measure res in real space, and I’d like to give it a go on my maps (particularly those where I am suspicious of the FSC-based res based on map appearance, or where I suspect overfitting). Is it available in any phenix package at present? The scripts site mentioned in the preprint (http://phenix-online.org/phenix_data/afonine/cryoem_validation/) is currently rather sparsely populated. (Also, I wonder whether a directional version of the d99 criterion might be useful to estimate anisotropic res in the case of a preferred orientation, analogous to the 3D-FSC approach of Yong-Zi Tan and Dmitry Lyumkis?) Cheers Oli

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rosetta refinement
by Sebastiano Pasqualato 24 May '18

24 May '18

Hi all, it seems that rosetta refinement uses test_flag_value=1 as default. Is there a way to change this? Couldn’t find it in the gui… Thanks s -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix comes with dials?
by Murpholino Peligro 17 May '18

17 May '18

[murph@localhost ~]$ dials.version DIALS 1.9.3-gb491019a-release Installed in: /home/murph/Bins/dials_stuff/dials-v1-9-3/modules/dials [murph@localhost ~]$ dials.version_1.13-2998 DIALS 1.8.0-gf5b6132-release Installed in: /home/murph/Bins/phenix_stuff/phenix-1.13-2998/modules/dials Why I never saw this on the documentation?

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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 15 May '18

15 May '18

Dear colleagues, Please see below an advert for the position of Protein Crystallography Facility Manager at the MRC Laboratory of Molecular Biology. Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 11th June 2018 For further details and information on how to apply please visit: https://mrc.tal.net/vx/appcentre-ext/candidate/post/1707/en-GB <https://mrc.tal.net/vx/appcentre-ext/candidate/post/1707/en-GB> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> Dr. Jan Löwe. E.mail: jyl(a)mrc-lmb.cam.ac.uk <mailto:[email protected]> _______________________________ Dr. David Barford Structural Studies Division MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH, UK. e.mail: dbarford(a)mrc-lmb.cam.ac.uk Tel. +44 (0)1223 267075

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Released: Phenix/DivCon Plugin - DivCon Discovery Suite v7.5.0
by Lance Westerhoff 10 May '18

10 May '18

Hello All- Some of you may have already seen this release, but I wanted to pass it along to the community as well. Today, we release version 7.5.0 of our flagship product: the DivCon Discovery Suite. This release includes fundamental improvements and a complete re-write of several key technologies leading to improved usability and a 14+ fold speedup to our Phenix/DivCon and XModeScore Crystallographic module for protomer/tautomer determination, fragment binding mode determination, and automated QM/MM X-ray refinement (including MOE-independent versions of each of those users who do not have MOE available). This version also includes a completely new tool for crystallographic "water picking" using 3DRISM. For a detailed breakdown of the new features (along with links to tutorials and other documentation), please see the following link: http://www.quantumbioinc.com/news/show/DivCon-7.5.0 As with prior releases, the software available for free for true non-profit/academic research. And of course it is available for industry use for a reasonable license fee. The list of available licenses (for electronic signature) is available here: http://www.quantumbioinc.com/products/software_licensing Thank you for your time and have a great rest of your spring! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

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European Crystallography Meeting Oviedo; Neutron Macromolecular Crystallography Satellite Meeting
by John R Helliwell 09 May '18

09 May '18

Dear Colleagues, We draw your attention to the following meeting in Oviedo, Spain in August:- https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php Best wishes, John and Matthew Emeritus Professor John R Helliwell DSc; Dr Matthew Blakeley, Institut Laue Langevin.

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Phenix.rosetta build Ubuntu 16.04
by Joseph Brock 08 May '18

08 May '18

Dear phenix community, I am trying to get phenix to run with rosetta on my Ubuntu 16.04 station. I am running the latest official phenix version (phenix-1.13-2998) and and compiled rosetta 3.7 (2016.32.58837) using scons as described: https://www.phenix-online.org/documentation/reference/rosetta_install.html https://www.rosettacommons.org/docs/latest/build_documentation/Build-Docume… Then ran rosetta.build_phenix_interface. All went without error but running rosetta.run_tests then gave the segmentation fault below. Defining variables as suggested did not help. I found a similar question in the phenixbb archives but no resolution: http://www.phenix-online.org/pipermail/phenixbb/2013-October/020274.html Any suggestions on how to move forward greatly appreciated! Cheers, Joseph. _________________________________________________________________________________________________________ Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Traceback (most recent call last): File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 305, in <module> run(sys.argv[1:], create_dir=True) File "/usr/local/phenix-1.13-2998/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 191, in run debug=params.output.debug) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 313, in __init__ self.run_jobs() File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 388, in run_jobs check_result(result) File "/usr/local/phenix-1.13-2998/modules/phenix/phenix/rosetta/refine.py", line 379, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1. Joseph S. Brock | PhD Researcher Drew Lab Department of Biochemistry and Biophysics Stockholm University

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