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Postdoc position in methods development at LBNL
by Dorothee Liebschner 22 Jan '20

22 Jan '20

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in computational methods development in the Molecular Biophysics and Integrated Bioimaging division at LBL. The overall objectives of the project are to develop theory and computation to extract conformational heterogeneity and disorder from diffraction and imaging data. The position is available immediately with an initial appointment for 2 years with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Qualified candidates must have a PhD in Biophysics, Physics, Mathematics, Chemistry, or related fields. https://lbl.referrals.selectminds.com/jobs/computational-biologist-postdoc-… ======================================================================== -- Project 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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Re: [phenixbb] How critical is ncs operator for real space refinement
by BuddySphinx 22 Jan '20

22 Jan '20

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How critical is ncs operator for real space refinement
by Yangqi Gu 21 Jan '20

21 Jan '20

Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

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Re: [phenixbb] How critical is ncs operator for real space refinement
by BuddySphinx 21 Jan '20

21 Jan '20

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isomorphous Fobs-Fobs maps
by Schulz, Eike-Christian 20 Jan '20

20 Jan '20

Dear all, we have recently tried to calculate isomorphous difference maps with phenix using the GUI. Unfortunately, we found that the results do _not_ seem to produce results that we would expect of a true difference map. Rather the resulting maps appear to show noise. We speculate that this is the result of _not_ scaling the datasets together. - Is this correct ? Applying the "multiscaling method" found in the advanced options changes the result, but it is still inconsistent with what we gain from e.g. the CCP4 procedures. Unfortunately, there is no online documentation to this tool. - Is there a way to scale the data to a reference before calculating the difference maps? - What is the proposed way of using this tool ? - Are there known bugs in the GUI version that are absent in the command line edition? With best regards, Eike

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Open scientist position at the EMBL-Grenoble - Project leader for ID30A/MASSIF-1 beamline upgrade
by Andrew MC CARTHY 13 Jan '20

13 Jan '20

Dear all, We have an open scientist position at the EMBL-Grenoble for a Project leader to oversee our contribution to the upgrade of the fully automated ID30A/MASSIF-1 macromolecular crystallography beamline at the ESRF. This is an exciting opportunity for an ambitious individual to join a team of scientists and engineers from the EMBL and ESRF in developing fully automated data collection protocols to maximise the scientific potential of the ESRF Extremely Brilliant Source upgrade. Closing date: Feb. 7th 2020. Interview date: March 6th, 2020 You can read more about the position and submit your application at: https://www.embl.de/jobs/searchjobs/index.php?ref=GR00139 Best regards, Andrew

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Postdoc position: Computational Algorithms combining Crystallography and WAXS for Drug Discovery
by Grant, Thomas 10 Jan '20

10 Jan '20

Dear PHENIX Community, Please share this notice with potential candidates. A post-doctoral position<https://www.ubjobs.buffalo.edu/postings/21288> is available immediately in the Grant Lab in the Department of Structural Biology at the University at Buffalo in Buffalo, NY, USA. Our group is currently seeking postdoctoral candidates to develop novel computational algorithms combining crystallography and solution scattering to aid in drug discovery. The successful completion of the project will impact many fields from drug discovery and development to basic biological processes. An excellent opportunity for creative, out-of-the-box thinkers who are self-motivated. Candidates will have the opportunity and support to present their research findings at national and international conferences and in high-impact scientific journals. The positions are for an initial term of two years with possibilities for renewal based on performance and available funding. Compensation will be commensurate with experience. Minimum Qualifications A PhD degree in structural or computational biology, chemistry, physics, mathematics, computer science or related fields. Preferred Qualifications Proficiency in computer programming, in particular Python. Excellent oral and written communication skills for presenting research at conferences and in scholarly journals. Background in physics or mathematics is a plus, in particular familiarity with concepts of Fourier transforms and diffraction. Experience with structural biology techniques such as crystallography and solution X-ray scattering is a plus. Apply Interested candidates can apply on the UBJobs website here: https://www.ubjobs.buffalo.edu/postings/21288 -- Thomas D. Grant, Ph.D. Research Assistant Professor Department of Structural Biology Jacobs School of Medicine and Biomedical Sciences<http://medicine.buffalo.edu/> University at Buffalo 955 Main Street, Room 5128 Buffalo, New York 14203 Email: tdgrant(a)buffalo.edu<mailto:[email protected]>

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3 years Postdoc positions Newcastle University, UK Prof. Nikolay Zenkin
by Arnaud Basle 06 Jan '20

06 Jan '20

Dear All, Please see the attached flyer and link below for 3-years postdoc position at Newcastle University. https://jobs.ncl.ac.uk/job/Newcastle-Research-Associate/577339301/ The positions are in Prof. Nikolay Zenkin's laboratory and informal enquiries should be directed to him (Nikolay.Zenkin(a)newcastle.ac.uk). Cheers, Arnaud -- Dr Arnaud Basle X-ray facilities manager Newcastle Structural Biology Laboratory Biosciences Institute Faculty of Medical Sciences Newcastle University Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 5482

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ISOLDE 1.0b4 released
by Tristan Croll 03 Jan '20

03 Jan '20

Happy new year to all my colleagues in the structural biology community! I'm delighted to announce the release of ISOLDE 1.0b4 to coincide with the stable release of ChimeraX 0.91. What is ISOLDE? ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments. Historically, this has been an extremely challenging task, since at low resolutions the maps alone are insufficient to precisely place individual atoms. ISOLDE aims to reduce this challenge in a number of ways: - Rebuilding is accomplished via GPU-accelerated interactive molecular dynamics (using OpenMM and the AMBER molecular dynamics forcefield) to make the task feel as close as possible to what it might be like to work with a real physical molecule. - Geometric validation of protein backbone and sidechain conformations is performed in real time, allowing you to see problem sites directly on the model as you work with it. - Remodelling can be performed by directly tugging on atoms, or via the interactive addition and removal of position, torsion and/or distance restraints - For crystallographic datasets, structure factors are constantly recalculated in the background as the model coordinates change - as the model improves, you see the map improve. For more details, see https://isolde.cimr.cam.ac.uk/. To install it for Linux, MacOS or Windows 10, go to http://preview.cgl.ucsf.edu/chimerax/download.html#release and install the **0.91** release build for your operating system. (IMPORTANT NOTES: this build of ISOLDE will **only** work with version 0.91 of ChimeraX. Additionally, Ubuntu users should use the "Generic Linux" ChimeraX build - the Ubuntu builds use compilers that are not compatible with ISOLDE). Start ChimeraX, go to Tools/More Tools... and follow the links to install ISOLDE. Equivalently, just type "toolshed install isolde" on the ChimeraX command line. You can then start ISOLDE via Tools/General/ISOLDE or the command "isolde start". If this is your first time using it I highly recommend running either or both of the first two tutorials found in the top left of the ISOLDE panel that will appear. A short list of what's new since 1.0b3: - source code for ISOLDE and its "sister" package ChimeraX-Clipper are now on GitHub at https://github.com/tristanic/isolde and https://github.com/tristanic/chimerax-clipper respectively. - integration with ChimeraX session save/restore framework. "save session.cxs" will save a snapshot of all models, maps and strucuture factors including all current ISOLDE restraints, and "load session.cxs" will return you to where you left off. - added new adaptive torsion restraint implementation (a periodic analogue to Geman-McClure distance restraints) to restrain protein torsions to their current geometry or to a reference model. For details, type "usage isolde restrain torsions" on the ChimeraX command line and click the link in the log. - documentation is now integrated with the ChimeraX documentation framework. In particular, "usage {command}" now provides a link to full documentation in the ChimeraX log window. - improved behaviour (speed and stability) of energy minimiser - significantly improved initial startup and simulation start times - clearer indication of simulation state (running/paused) - remote Python interface for communication with other packages - various improvements and bug-fixes to handling of crystallographic data. In particular: better handling of anisotropic datasets, and improved stability of bulk solvent and scaling calculations. - improved performance of live crystallographic map updates. - support for multiple independent sets of adaptive distance restraints (currently only available via the Python API). For example, one set may be used to maintain internal geometry, while another represents crosslinking/mass spec or evolutionary coupling restraints. - "Demo" button on ISOLDE GUI retired and replaced with a "Tutorials" drop-down menu. - added tugging support in ChimeraX VR (thanks to Tom Goddard). ChimeraX currently supports VR only in Windows.

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Adding a command line run job to the GUI job history
by Ahmad Khalifa 27 Dec '19

27 Dec '19

Hello, I ran a real space refinement job using the command line and an effective parameters file. Is it possible to link this job again to the Phenix GUI? How? Regards.

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