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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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Postdoc position, Sugar Transporting Membrane Proteins (Denmark), repost
by Bjørn Panyella Pedersen 30 Mar '20

30 Mar '20

Dear colleagues, Repost of our postdoc position. Deadline is in 3 days. Please pass this along any one who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://tiny.cc/MBG_postdoc We are looking for a highly skilled and motivated postdoc with an interest in working on sugar transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2020, but starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. Deadline: All applications must be made online (http://tiny.cc/MBG_postdoc) and received by 2. apr. 2020.

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insert ligand restraints in real space refinement
by Valerie Biou 27 Mar '20

27 Mar '20

Hello I am trying to impose restraints on my lipid ligand during real space refinement. I found the command refinement.geometry_restraints.edits.scale_restraints { atom_selection = "resname LLP" scale = 2.5 apply_to = *bond *angle dihedral chirality I have 2 questions 1) can those lines be called from the GUI and where? if not, how can I insert them in a previous command file? 2) what do the * stand for? is it to activate or cancel the selection of an item? sorry if those questions have been asked before, I can't find the command to browse the bb archive. All the best, Valérie

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Raw diffraction images for SARS-CoV-2 related structures
by Gerard Bricogne 27 Mar '20

27 Mar '20

Dear all, It is a pleasure to be able to end the (GMT) week by calling for a huge round of applause for the Diamond team, who this afternoon started uploading a large collection of sets of raw diffraction images (77 as we write but the upload is still ongoing) for PDB entries that were released two days ago. Special thanks to Graeme Winter who organised the upload to Zenodo. The datasets are collectively accessible via the following link: https://zenodo.org/search?page=1&size=20&q=keywords:%22SARS-CoV-2%20main%20… Graeme asked that "major kudos [be given] to Zenodo developers who have been very responsive with helping us do automated downloads". Happy scrutiny and reprocessing of these datasets, and re-refinement of the associated structures, to all hard-core MX addicts! With best wishes, Clemens & Gerard. -- On Thu, Mar 19, 2020 at 10:00:11AM +0000, John Berrisford wrote: > Dear all > > The wwPDB OneDep system allows depositors to provide DOIs of raw > diffraction images during deposition to the PDB and once again > encourages depositors to provide a DOI for raw images when they have > submitted. > > Out of the 9665 X-ray entries that were released in 2019 we have DOI's > for raw images in 205 of these entries. > > We would encourage depositors to provide the DOI for their raw images > when they are available. > > Regards > > John > > > On Mar 19 2020, at 9:48 am, Joel Sussman <joel.sussman(a)WEIZMANN.AC.IL> wrote: > > > 19-Mar-2020 > > Dear Loes, Peter, Clemens & Gerard, > > I concur that it is crucial to preserve the original diffraction data > > and make it available to anyone who would like to use it. > > As an example, please see the very recent paper by > > Nachon et al (2020). "A second look at the crystal structures of > > Drosophila melanogaster acetylcholinesterase in complex with tacrine > > derivatives provides Insights concerning catalytic intermediates and > > the design of specific insecticides" Molecules 25 pii: E1198 > > [https://www.ncbi.nlm.nih.gov/pubmed/32155891]. > > The study reexamines the original data, with modern software tools, > > the original data of a paper we published in 2000 (~20 years ago) and > > revealed features that had not been noticed. Specifically > > 1) previously unmodeled density in the native active site can be > > interpreted as stable acetylation of the catalytic serine. > > 2) Similarly, a strong density in the DmAChE/ZA complex, originally > > attributed to a sulfate ion, is better interpreted as a small molecule > > that is covalently bound. The complex is reminiscent of the > > carboxylate/BChE complexes observed in crystal structures of hBChE > > [Brazzolotto et al, 2012; Nicolet et al, 2003], and demonstrates the > > remarkable ability of ChEs to stabilize covalent complexes with carboxylates. > > Thus, the study demonstrates that updated processing of older > > diffraction images, and the re-refinement of older diffraction data, > > can produce valuable information that could not be detected in the > > original analysis, and strongly supports the preservation of the > > diffraction images in public data banks. > > Best regards > > Joel > > ------------------------------------------------------------------------------------ > > Prof. Joel L. Sussman. Joel.Sussman(a)weizmann.ac.il www.weizmann.ac.il/~joel > > Dept. of Structural Biology tel: +972 (8) 934 6309 proteopedia.org > > Weizmann Institute of Science fax: +972 (8) 934 6312 > > Rehovot 76100 ISRAEL mob: +972 (50) 510 9600 > > ------------------------------------------------------------------------------------- > > > > > >> On 19 Mar 2020, at 11:32, Kroon-Batenburg, L.M.J. (Loes) > >> <l.m.j.kroon-batenburg(a)UU.NL> wrote: > >> > >> Dear Gerard, > >> > >> This is a great idea. Of course I am very much in favour of making > >> available raw diffraction images, and such a virtual workshop could > >> demonstrate the usefulness of reprocessing raw diffraction data and > >> structural refinements. I am not at all afraid that archiving of raw > >> data that are the basis of a scientific paper will have significant > >> environmental effects: this is minor compared to our everyday use of > >> cloud services. And as Graeme mentioned: when archiving raw data > >> make sure to add sufficient and correct meta data. > >> > >> Best wishes, > >> Loes > >> > >> ___________________________________________________________ > >> Dr. Loes Kroon-Batenburg > >> Dept. of Crystal and Structural Chemistry > >> Bijvoet Center for Biomolecular Research > >> Utrecht University > >> Padualaan 8, 3584 CH Utrecht > >> The Netherlands > >> > >> E-mail : l.m.j.kroon-batenburg(a)uu.nl > >> phone : +31-30-2532865 > >> fax : +31-30-2533940 > >> > >> Van: CCP4 bulletin board <CCP4BB(a)JISCMAIL.AC.UK> namens Gerard > >> Bricogne <gb10(a)GLOBALPHASING.COM> > >> Verzonden: woensdag 18 maart 2020 23:30 > >> Aan: CCP4BB(a)JISCMAIL.AC.UK <CCP4BB(a)JISCMAIL.AC.UK> > >> Onderwerp: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures > >> > >> Dear colleagues, > >> > >> Perusal and some initial (re-)refinement of the various SARS-CoV-2 protease > >> structures in the PDB seems to indicate that that there might be potential > >> to improve these if refinements could be repeated after some reprocessing > >> and further analysis of the raw diffraction images, rather than > >> against the > >> deposited merged data. This statement should in no way be construed > >> as a > >> criticism of the remarkable achievements of the research groups concerned, > >> who have been operating under tremendous time pressure, but as an exciting > >> opportunity to push methods to their limits on a uniquely significant class > >> of structures. > >> > >> Another consideration is that the various logistical problems created by > >> COVID-19 may soon make it increasingly difficult to collect new diffraction > >> data on potential drug targets relevant to the fight against SARS-CoV-2, > >> underlining the importance of ensuring that the best results be obtained > >> from every dataset actually collected, and that the most useful conclusions > >> be drawn from the analysis of those datasets towards improving the quality > >> of subsequent data collections. > >> > >> On this basis we would like to propose that special efforts be made > >> to grant > >> public access to the raw image data associated with any SARS-CoV-2 related > >> structure that is deposited into the PDB. This can be done by (1) archiving > >> these raw image data using resources such as data.sbgrid.org, zenodo.org, > >> proteindiffraction.org or any other cloud-based data-sharing service, and > >> (2) communicating the corresponding DOIs to the wwPDB centres. This idea > >> could be extended to datasets that investigators would like to offer to > >> interested methods developers or expert users at the pre-deposition stage. > >> > >> Experts making use of those raw data would be encouraged to document, > >> in as > >> much detail as possible, how particular programs or workflows could > >> be used > >> on those structures/datasets to obtain the best results. This would > >> be a > >> kind of "virtual workshop", a particularly valuable collective > >> activity at > >> the present time when several in-person workshops (e.g. RapiData) > >> have been > >> cancelled and many meetings are in limbo for several months. > >> > >> The latter activity would benefit from having a centralised facility > >> set up > >> for the experts to post their results and annotations: we could > >> create such > >> a facility, but other, larger groups might want to consider doing so. > >> > >> > >> With best wishes, > >> > >> Clemens & Gerard. > >> > >> ######################################################################## > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

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