- phenixbb - phenix-online.org

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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phenix server down?
by Murpholino Peligro 02 May '18

02 May '18

Is the phenix server down? I cannot access the following links http://www.phenix-online.org/documentation https://www.phenix-online.org/download/phenix/release/ :(

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Introducing ISOLDE
by Tristan Croll 01 May '18

01 May '18

Dear members of the structural biology community, It is with great pleasure that I announce the release of version 1.0b1 of ISOLDE, a new, free for academic/nonprofit use, environment for interactive rebuilding of macromolecular models against low-medium resolution experimental crystallographic or cryo-EM maps. A paper describing ISOLDE is online at http://scripts.iucr.org/cgi-bin/paper?S2059798318002425, and you can also get an overview from my demonstration video at https://www.youtube.com/watch?v=limaUsNAVL8. In brief, though, ISOLDE is designed to help overcome the substantial challenge involved in building high-quality models into “difficult” maps (e.g. those with worse than 3Å resolution) by re imagining the task as one akin to interacting with a real, “living” molecule. At its heart is the use of interactive molecular dynamics: all atoms feel van der Waals and electrostatic interactions with their neighbours as you interact with them, avoiding clashes and constantly settling towards their nearest low-energy state. In addition to this, ISOLDE helps interpret what you're looking at by performing real-time rotamer, Ramachandran and peptide plane validation, flagging up potential problems directly on the model to give you instant feedback on the results of your actions. Specific features: - support for protein, nucleic acid, water and some small molecules/ions (with substantially expanded support to come in later versions) - start an interactive simulation covering anything from a few residues to your entire model (depending on your hardware) at the click of a button - “always-on” validation updates every time coordinates change (results are shown directly as markup on the model itself, and also accessible via more traditional tables/plots) - Interactively apply peptide plane or cis/trans flips and add/remove position, distance, rotamer and secondary structure restraints via a simple graphical interface - Smoothly shift any continuous stretch of backbone forward/backward along the chain to easily recover from register shift errors - Save a checkpoint in a running simulation and return to it with a button click, allowing you to experiment with tricky regions without fear - Real-time visualisation of crystal symmetry contacts: when the master atoms move, they move. - One-button masking of maps to cover any arbitrary atom selection – particularly useful for diagnosing large-scale problems. - Extensive GUI and API documentation, available by clicking the “Help” button in the ISOLDE GUI window. ISOLDE is built as a plugin to UCSF ChimeraX (http://preview.cgl.ucsf.edu/chimerax/download.html) and is currently available for modern Linux distros and MacOS, and can be installed from within ChimeraX via its ToolShed (Tools/More Tools...). It should run on any Linux version that supports ChimeraX itself. NOTE: due to some recent changes in the ChimeraX API, the current build will only work with the ChimeraX 0.6 release (not the version 0.7 daily builds). In terms of hardware, ISOLDE is designed based on the understanding that not everybody has access to high-performance computing facilities, so its minimum requirements are as modest as possible. The most important requirement is a GPU capable of OpenCL 1.2 or CUDA processing. My “go-to” machine for performance testing is a 2016-model gaming laptop equipped with a Nvidia GTX 1070 GPU – this achieves ~20 coordinate updates and >30 graphics updates per second with live validation on the included 229-residue demo model, indistinguishable from (or slightly faster than) my Xeon workstation. At the other end of the scale, it runs at usable speeds on my MacBook Air for simulations of a few dozen residues, sufficient for many tasks. I hope you find it useful, and enjoy using it as much as I've enjoyed making it. The MolProbity score to beat on the demo model is 1.02 (after refinement in your favourite package – ID is in the PDB header so you can download reflections from the wwPDB), and bonus points if you can identify the mystery ligand (I can't). If you recognise it as your model I apologise – I picked it out at random, I swear! Best regards, Tristan

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DNA pucker
by Dyda 30 Apr '18

30 Apr '18

Hi, Is it possible and if so how to change the pucker restraint for a particular DNA nucleotide from C2'-endo to C3'-endo in phenix.refine? I have a problem with a terminal nucleotide that is in an active site and the current C2'-endo doesn't seem consistent with the 2Fo-Fc map. Thanks for your help. [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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