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Two Ph.D. studentships at Newcastle University, UK Prof. Bert van den Berg
by Arnaud Basle 13 Apr '20

13 Apr '20

Dear All, Please see the attached documents for two Ph.D. studentships at Newcastle University, UK. The positions are in Prof. Bert van den Berg's laboratory and informal inquiries should be directed to him (Bert.Van-Den-Berg(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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Postdoctoral position in the Korostelev Lab
by Loveland, Anna 12 Apr '20

12 Apr '20

Postdoctoral position open at the University of Massachusetts Medical School, in the Korostelev Lab: https://www.umassmed.edu/korostelev-lab/. We study translation regulation, using cryo-EM and biochemistry. We are particularly interested in: (1) Translation accuracy; (2) Ribosome's central role in bacterial stress signaling and gene regulation; (3) Neurodegenerative and other diseases, which originate from dysregulation of translation. References to some lab publications are provided below. Our laboratory is housed at the RNA Therapeutics Institute, a vibrant and highly interactive research community: https://www.umassmed.edu/rti/about-the-rti/faculty-members/. Our colleagues are interested in nearly all aspects of RNA biology, from small to large RNAs to RNA chemistry and therapeutics development. We seek a highly motivated person who very recently received a PhD, or will soon receive a PhD. Applications sent prior to the dissertation defense date are welcome. Please submit the following information via email to: ann.powers(a)umassmed.edu 1) your CV (including publication list); 2) in less than 2 pages, an outline of your: (i) previous work - focusing on your most interesting finding(s); (ii) your current/future scientific interests, and whether/which aspects of translation regulation sound interesting to you; 3) email addresses of three references. Selected publications (accessible via the provided links): - Svidritskiy et al. “Extensive ribosome and RF2 rearrangements during translation termination<https://elifesciences.org/articles/46850>”. eLife.2019. - Loveland et al. “Ensemble cryo-EM elucidates the mechanism of translation fidelity<https://www.nature.com/articles/nature22397>”. Nature. 2017. - Demo et al. “Structure of RNA polymerase bound to ribosomal 30S subunit<https://elifesciences.org/articles/28560>”. eLife. 2017. - Abeyrathne et al. “Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896748/>”. eLife. 2016. - Loveland et al. “Ribosome•RelA structures reveal the mechanism of stringent response activation<https://elifesciences.org/articles/17029>”. eLife. 2016. --- Anna Loveland, Ph.D. anna.loveland(a)umassmed.edu 617 610 4321 (cell) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

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Problem with molecular replacement
by Shramana Chatterjee 09 Apr '20

09 Apr '20

Hi, I am trying to solve a structure using a data solved by SAD as an reference (ensemble in phaser). The structure I am trying to solve has 100% sequence identity with the solved one. The problem that I am facing during Phaser MR is that, in the solved structure there are 6 molecules in the ASU although I am getting maximum 4 molecules in the ASU and also Rfree is around 0.49 just after the phaser. Phaser is showing a good values of LLG (>500) and TFZ (>8). It would be very helpful if I get any suggestion about the above-mentioned problem. Thank you in advance.

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Re: [phenixbb] Problem with molecular replacement
by Shramana Chatterjee 09 Apr '20

09 Apr '20

Thanks Roger. I am trying through looking at packing of crystal lattice.It seems that there are some gaps in the lattice. May be this is identical with the solved one because of identical cell dimension and space group. Although I think I should cross check with lattice as Matthew's analysis suggest a different number of copies. On Thu, Apr 9, 2020 at 8:51 AM Roger Rowlett <rrowlett(a)colgate.edu> wrote: > For MR solutions with more than 4 molecules in the ASU, you can improve > your chances of finding a solution by employing the following > considerations: > > The number of protein units in the ASU predicted by Matthew's analysis my > not be accurate for n>4. Always look at the molecular packing of potential > solutions in the ASU using Coot or Pymol. You may discover you have too > many molecules, and therefore overlaps, or too few molecules, leaving > protein size gaps in the crystal lattice. Lattice packing of partial > solutions may guide your thinking about the correct number of molecules in > the ASU. A good solution should normally have symmetrical and clear solvent > channels, and good contacts between all molecules. > > You may nave a better chance of obtaining a initial solution by searching > with dimers (if structurally appropriate) than monomers. > > Unless your crystal form is identical to the solved version, there is no > guarantee your N will be the same as the solved N molecules in the ASU. Use > the Matthew's analysis and lattice packing as your guide. > > Using this approach I've been able to obtain MR solutions for ASUs with > N=6-8, even with identities as low as 30%. > > Good luck. > > Roger Rowlett > Gordon & Dorothy Kline Professor, Emeritus > Colgate University > > > On Wed, Apr 8, 2020, 11:43 PM Shramana Chatterjee <schatter90(a)gmail.com> > wrote: > >> Hi, >> >> I am trying to solve a structure using a data solved by SAD as an >> reference (ensemble in phaser). The structure I am trying to solve has 100% >> sequence identity with the solved one. The problem that I am facing during >> Phaser MR is that, in the solved structure there are 6 molecules in the ASU >> although I am getting maximum 4 molecules in the ASU and also Rfree is >> around 0.49 just after the phaser. Phaser is showing a good values of LLG >> (>500) and TFZ (>8). >> >> It would be very helpful if I get any suggestion about the >> above-mentioned problem. >> >> Thank you in advance. >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > >

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refinement of EM models with hydrogens using phenix.real_space_refine
by Coudray, Nicolas 09 Apr '20

09 Apr '20

Hi all, We had a question regarding how the phenix.real_space_refine works when used to refine CryoEM models with hydrogens: are hydrogens treated as riding or are they explicitly refined? Regards, Nicolas

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LINK to chromophore
by 김경현[ 교수 / 생명정보공학과 ] 06 Apr '20

06 Apr '20

Hi, I get linking problems of the CRF chromophore in GFP, where the peptide bonds connecting to each end of the chromophore to the protein do not show planar configuration. The LINK cif seems to only constrain bonds and angles. Any help how to fix the planar peptide bonds at the connecting ends? Many thanks. Regards, Kyung hyun == Prof. Kyung Hyun Kim, Ph.D. Rm 244 R&D Center Green Campus Korea University Anam dong, Sungbuk gu, Seoul 136-701 Department of Biotechnology & Bioinformatics Korea University Sejong Campus, Sejong, Korea Tel : +82 2 3290 3444, +82 10 9014 1416 Homepage : *sbl.korea.ac.kr <http://sbl.korea.ac.kr>*

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ISOLDE 1.0b5 release
by Tristan Croll 06 Apr '20

06 Apr '20

Hi all, For those still lucky enough to be working on molecular model building during this crisis, I've just pushed ISOLDE 1.0b5 out to the ChimeraX ToolShed (to work with the ChimeraX 0.93 release version - download from http://preview.cgl.ucsf.edu/chimerax/download.html#release, then install ISOLDE from within ChimeraX via Tools/More Tools...). While development has been a little light since version 1.0b4 due to travel in February and then, well... everything since, there are a few new features and bug-fixes worth downloading for: - Perhaps the biggest improvement isn't actually mine - thanks to some stellar work by Tom Goddard at UCSF, ChimeraX's ribbon drawing is now ten times faster than before. Particularly for those working with very large models, this drastically reduces the lag time upon finishing an interactive simulation and returning to the default display mode. - I've done some optimisations to the methods for choosing the initial map contour levels and the MDFF coupling constant (how strongly the map "pulls" on the model during simulations). They're now about 20 times faster, removing most of the delay on initial preparation of a model for ISOLDE. - If you're lucky enough to be working on a multi-GPU machine, you can now explicitly specify the GPU to use for simulations with the command "isolde set gpuDeviceIndex {a number}" (you may need to experiment to work out which GPU is which) - You can adjust the number of simulation steps between GUI updates with "isolde set timeStepsPerGuiUpdate". This is particularly useful for slower GPUs - your simulation won't actually run faster, but your experience of it will be much smoother. The default value of 50 works well for high-end GPUs; for (for example) light-weight MacBook GPUs a value of 10 may be more suitable. Performance curves for a few of the machines available to me can be found at https://isolde.cimr.cam.ac.uk/performance-benchmarks/. - The command "clipper symmetry #{model number}" will draw a unit cell with all rotational symmetry and screw axes (mirror symmetry is not yet handled). The depiction is still a work in progress, but the fundamentals are there. - While not new to 1.0b5, a reminder that since 1.0b4 ISOLDE is fully compatible with ChimeraX's session save/restore. The command "save {filename}.cxs" will save your current session (including your model(s), all custom restraints, maps, weightings and visualisation state) to a file which can be reopened on the same or another machine to pick up exactly where you left off. Known bug: (seemingly only) on Linux machines, certain links to the help files (e.g. by typing "usage isolde" on the command line and then clicking the "isolde adjust distances"link in the log) sometimes cause segmentation faults if the help browser is not already open, crashing ChimeraX. This appears to be a bug in the Qt 5.12 web browser implementation, but so far has proven near-impossible to isolate. To avoid it, simply make sure the help browser is open (Help/User Guide) before clicking any links in the log. I very much hope you find it useful. Stay healthy! Tristan

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Update on COVID-19 Open Structures initiative
by Randy Read 03 Apr '20

03 Apr '20

Dear all, Last week I posted the message below, suggesting an open science approach to ensure that there will be no unnecessary delays in the determination of crystal structures related to COVID-19, whether they’re from the SARS-CoV-2 virus, interacting host proteins, or complexes. Working together, and combining expertise in data analysis, structure determination and computational modelling, we believe we can greatly accelerate progress on difficult structures. Since last week we’ve chosen a platform, Microsoft Teams, to coordinate the effort, created a new Team and built the bare bones of a site ready for new targets. (For those who prefer other collaboration platforms such as Slack or Zulip, they might well have advantages but I had easy access to the Teams infrastructure and we’re already using it for working from home.) If you believe that you can bring expertise to this initiative and you’re willing to share your insights and any promising results immediately with others, please get in touch and I’ll add you to the team. If you have diffraction data for a target structure for this initiative, please send an email to me, to Massimo Sammito (mds83(a)cam.ac.uk) and to the CASP organisers (casp(a)predictioncenter.org). Either Massimo or I will add you to the team, upload the target data, links and other information and send an alert to everyone who has registered. Best wishes, Randy Read =========== The Covid-19 crisis is bringing out the best in the communities we belong to, with many people giving deep thought to how we can use our skills to help. On the crystallography bulletin boards we've seen offers to help in solving Covid-19-related structures that prove difficult, offers to help with improving protein stability, suggestions that the deposition of raw diffraction images would allow the community to help get the best possible version of any relevant structure, and requests to share bioinformatics analyses and predictions of what are the most interesting targets. We're writing to suggest an additional way that the community can help to accelerate progress in the structural understanding of Covid-19. The CASP (Critical Assessment of Structure Prediction) organisers have recently launched an initiative to mobilise the structure prediction community to predict and refine 3D structures of SARS-2-Covid proteins and relevant complexes that either have unknown structure or are non-trivial modelling targets: http://predictioncenter.org/caspcommons/index.cgi. Note that the models will be refined much more extensively than typically done in a normal CASP round, which should make them even better than the impressive results seen in recent years. We would like to build on this initiative, and the enthusiasm this has revealed in the prediction community, to help to accelerate the determination of structures needed for a molecular-level understanding of Covid-19. Structure prediction has reached a level of maturity where predicted ab initio models and distant homology models can be accurate enough to solve new structures by molecular replacement. The best way to bring the prediction and experimental communities together to exploit these developments and accelerate progress is to embrace an open science approach. To that end, we propose the following: * If you have diffraction data involving a SARS-2-Covid protein, a host protein relevant to pathogenesis or a complex, but you are not immediately able to solve the structure, contact the CASP organisers (casp(a)predictioncenter.org) with the sequence(s) of the construct(s) that went into the crystallisation drop. If relevant predictions have already been made, any unreleased models will be released at this point (along with predictions of local accuracy). If proteins in your crystals are not already modelling targets, the CASP organisers will consider them as potential new targets for the modelling community. * We all want the fastest possible progress on scientific understanding of Covid-19, and this can best be achieved by completely open science. On a number of occasions at crystallographic computing schools and workshops, we have seen extremely difficult structures yield to the combined expertise of a number of developers and "power users" of the software, none of whom knew how to solve every problem that arose. Even before CASP models are available, some other crystallographer may find a way to solve the structure! So it would be ideal if the sequence information you provide to the CASP organisers was accompanied by a DOI or URL pointing at the diffraction data, preferably in the form of raw images as well as integrated data. Data from different crystal forms or poorly isomorphous crystals can also be incredibly valuable. Openness should go both ways, so people who wish to access these data will be asked to agree to immediately release any positive results, even if these fall short of a full structure solution, so that others can build on them. Best wishes, Randy Read (in cooperation with the CASP organisers) ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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<no subject>
by Werther, Rachel A 02 Apr '20

02 Apr '20

Dear All, My colleague and I are troubleshooting a Phaser run that her Phenix was not able to solve but mine was. We both use the Graphical User Interface, and we both use the current version, Phenix 1.17.3644 Her log file shows “ELLG TARGET 120” and “RFACTOR CUTOFF 35.00”. If these settings are the reason one run gave the right solution and the other didn’t, how do we access and change these settings? I attached both the log files. Right.log gave the right solution, Wrong.log gave the wrong solution. Many thanks, Rachel Werther Rachel Werther / Research Technician III / Stoddard Lab / Basic Sciences / Fred Hutchinson Cancer Research Center / rwerther(a)fredhutch.org<mailto:[email protected]> / 206-667-4066

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COVID-19 protease inhibitors - 2nd call for designs - Thurs midnight
by Frank von Delft 01 Apr '20

01 Apr '20

All - last week's call for compound designs to the CoV-2 main protease (https://covid.postera.ai/covid) elicited an astonishing response... (I confess I was quite taken aback.) I just realised I should let this BB know the second call for designs is now open. *Deadline is tomorrow 23:59 PST (April 2nd). *(Apologies for those that weren't following on twitter.)* *Two things: * we're asking for designs especially focusing on covalent inhibitors (read more here <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-track…>) * the most convincing designs will be fast-tracked by spending more money to cut several weeks off the testing (read more here <https://discuss.postera.ai/t/screening-cascade-fast-track-and-regular-track…>) Happy designing! Frank

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