- phenixbb - phenix-online.org

<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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Public resource for the structures, validation and re-modelling of Corona virus macromolecules
by Andrea Thorn 27 Mar '20

27 Mar '20

Dear colleagues, we are methods developers in structural biology. During this time of crisis, we decided to put our brains to where our hearts are and have started a public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2: https://github.com/thorn-lab/coronavirus_structural_task_force It can be used to download all relevant structures, look at structural validation information, diagnostic data for the quality of experimental data and available re-refinements. We will expand this resource in time, but as of today, it contains all deposited SARS-CoV and SARS-CoV-2 structures, sorted by protein and virus, PDB-REDO entries, diffraction data diagnostics from AUSPEX and PHENIX.XTRIAGE, WHATCHECK reports and Tristan Croll's fantastic manual ISOLDE re-refinements. We will soon add MOLPROBITY to lighten the traffic on the server at Duke, individual links to Global Phasing's efforts in re-processing and re-refinement of individual structures and HARUSPEX map annotations for the Cryo-EM structures. We may point out potential improvements in some structures in these data, but this is not meant as criticism of the achievements of the researchers who first elucidated these structures! It merely reflects on recent progress in methods development and the potential to push our methods to their limit in order to get every last bit of biological information from a given data set. We hope this can make a (small) difference for a cure of COVID-19. If you have any questions or would like to contribute, please let me know! Andrea Thorn. The collaborators, as of today, are: myself, Yunyun Gao, Kristopher Nolte, Ferdinand Kirsten, Sabrina Stäb (RVZ, University of Würzburg, Germany) Gianluca Santoni (European Synchrotron Facility, France) Tristan Croll (CIMR, University of Cambridge, UK) The Richardson Laboratory (Duke University, USA) We would also like to thank for their advice: Sameer Velankar, James Holton, Manfred Weiss, Gerard Bricogne, Clemens Vonrhein and Robbie Joosten. -- Dr. Andrea Thorn | group leader andrea.thorn(a)uni-wuerzburg.de +49 931 31-83677 Rudolf Virchow Center, University of Wuerzburg Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

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How to generate LLG map
by afshan begum 26 Mar '20

26 Mar '20

Dear expert, I have collect the data with the bound ligand at 1.4 Å . The ligand contain the sulphate molecule in its ,how could we generate the anamolous signal of sulphate ion to confirm its presence in the structure, actually there are very clear density of the full ligand molecules except for the SO3 ion . As I did it before via phenix but I completely forget it was 4 years ago I used to generate the LLG map for the presence of chloride ion . Many thanks Afshan Sent from my iPhone

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COVID-19 - help design protease inhibitors - 1st round Thurs midnight
by Frank Von Delft 25 Mar '20

25 Mar '20

To all you structural biologists locked out of your labs, bored with answering emails or writing your non-COVID paper, and itching all your lives to be medicinal chemists, here's your chance: https://covid.postera.ai/covid And you get to do something directly on COVID too. It's easy: * stare at the pile of fragments we found bound to the SARS-CoV-2 Main Protease in our somewhat epic XChem fragment screen<https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-a…> this month (alluded to by others) * see if you can spot cool ways of (especially) merging those hits - or anything else * draw the compound onto that page * hit submit It's actually a bit harder than it sounds - so we're betting that many brains will crack the nut of hitting potency in one go (!). We will do the rest - well, we'll try, if the Filters Approve and the Funds Permit -- and even for that, you can contribute, or tell people that could contribute (details on that page). First collection closes tomorrow (Thurs) midnight Pacific Time (but there will be more). Yes, it is a huge social experiment and a total crapshoot - but we must do something! So thank you for all and any help... *** Do forward to anybody relevant, especially experienced medicinal chemists. *** If you know virology labs set up to do SARS-CoV-2 assays, email the address on that page. *** If you have help to offer or wisdom to share, do so on the forums on that page *** If you want to use the data for anything else - PLEASE DO - we were anxious to push it out ahead of PDB release cycle or getting preprint written. Frank -- Prof Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1 and XChem Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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Rapid access to COVID-19 related fragment screening
by Fearon, Daren (DLSLtd,RAL,LSCI) 25 Mar '20

25 Mar '20

Dear all, As part of Diamond's effort to combat COVID-19, we are offering fragment screening expertise and infrastructure to users working on COVID-19 related targets (as demonstrated by the recent fragment screening campaign against SAR-CoV-2 Main protease<https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-a…>). In order to submit a proposal for COVID-19 related research please complete the Rapid Access Form<https://fs3.formsite.com/DiamondLightSource/nynlkya9ks/index.html> and send a completed XChem Application Form<https://www.diamond.ac.uk/dam/jcr:690e7c9d-7b4c-4a7d-bc58-9101e9af4df8/XChe…> to covid19access(a)diamond.ac.uk<mailto:[email protected]>. Due to access and travel restrictions, experienced XChem staff will prepare samples on-site, organise unattended data collection and analyse the data using the XCE pipeline. All data will then be made available to the users and as open access through Fragalysis <https://fragalysis.diamond.ac.uk/viewer/react/landing> and the Diamond webpage. Further details regarding crystal system requirements, available fragment libraries and screening protocols can be found here<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html>. Kind regards, Daren Dr Daren Fearon XChem Beamline Scientist Diamond Light Source Ltd Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE Tel: 01235 778936 Email: daren.fearon(a)diamond.ac.uk<mailto:[email protected]> Web: www.diamond.ac.uk<http://www.diamond.ac.uk/> -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Covid-19: open science to harness synergies in structure prediction and structure solution
by Randy Read 24 Mar '20

24 Mar '20

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 ----- 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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Re: [phenixbb] [ccp4bb] Se SAD phasing map becomes worse after refinement
by Randy Read 24 Mar '20

24 Mar '20

Dear Zhu, Questions specific to Phenix should really go to the Phenix-BB, so I am cross-posting my reply there. Here I’ll focus more on generic issues. There are also CCP4 tools that you could consider and presumably other people will offer advice on those. One point you raise comes up so much that we have an entry in our FAQ (https://www.phaser.cimr.cam.ac.uk/index.php/FAQ) about it: “Can I use Phaser to check the correctness of a model I have already built and refined?” The answer is no, because once you’ve refined the model it becomes better than random at predicting the data and therefore achieves a high LLG score, regardless of whether or not it is correct. In this case, you might be able to use Phaser to help complete the model if one of the two copies of the complex is more completely modelled than the other. If, say, you had a model for one copy you could fix that and search for a second copy: this should work because the refinement didn’t know anything about the second copy. Phenix.autosol attempts to determine the NCS operators, so you need to check whether that has succeeded. If not, you might need to try some more manual approaches to defining the NCS, which would help a great deal in map improvement. Tom Terwilliger might answer this in more detail (perhaps on the Phenix-BB), but I don’t think you can build protein and nucleic acid in the same job, so you should look at the documentation to see how to do that. Good luck! Randy Read ----- 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 > On 24 Mar 2020, at 04:31, Zhu Qiao <jasonqiao03(a)GMAIL.COM> wrote: > > Dear All > > I am sorry for the long context. > > I have one protein (252 AAs, 2 Met) bound to double-stranded DNA (24 bp) crystalized. I collected the Se-Met data of the crystal in C222 up to 2.8 angstrom. the space group is confirmed by running the pointless. > > I used the Phenix.Autosol to find the heavy atoms and get a quite nice map after the density modification. It seems there are two proteins and two DNA duplex are in one ASU. Phenix.Autobuild can only build less than half of the protein sequence into the map and fill in the potential DNA map with amino acids. The Rwork/Rfree is 0.40 and 0.46, with the map CC=0.60. If I do the MR with the initial model built by Autobuild, the result TFZ=40, LLG=200+, which suggests the partial correction of the initial model. > > Here is the problem. From the map, I can see one of my protein domain and a clear feature of DNA double helix. But whatever I go further for manual build using coot, like building the DNA double-strand into the map and building the resolved domain, the refinement statistics go bad with R free ~0.50. > > I am wondering what's going wrong and how come the refinement can't improve the R factor. > > I have attached the relevant photos. > https://drive.google.com/drive/folders/1dJ4kn7CEHkCL3sMcCJtBqa5OsVFQngBx?us… > > > Sincerely > Zhu > > ######################################################################## > > 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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New cctbx conda packages for testing
by Billy Poon 20 Mar '20

20 Mar '20

Hi everyone, Sorry for the long delay, the current Phenix release and helping out with an experiment at SACLA earlier in the year, took priority. But I have been able to clean up the cctbx conda packages that I built at the end of last year. The major differences are as follows. 1) Windows packages are available for Python 2.7, 3.6, and 3.7. It's not clear why conda-build is having issues with Python 3.8, so I'm still sorting it out. 2) The full repositories are copied now. As a consequence, you'll be able to run some tests like "libtbx.run_tests_parallel module=cctbx nproc=24" and all the tests will run. 3) The LIBTBX_BUILD environment variable is no longer needed, so it is not set on activation of the conda environment. 4) The libtbx.configure and libtbx.refresh commands are removed from the conda package until the ability to configure/build against the conda installation of cctbx is available. Currently, those commands will break the environment. The linux and macOS packages support Python 2.7, 3.6, 3.7, and 3.8, just like before. The command to create a new environment is, conda create -n test -c cctbx-dev cctbx python=<python version> If "python=<python version>" is left out, the default Python version will be 3.8. To install cctbx into the currently active conda environment, the command is, conda install -c cctbx-dev cctbx The packages are currently on the cctbx-dev channel, but the goal is to get official packages into conda-forge. To get the cctbx recipe into conda-forge (https://github.com/conda-forge/staged-recipes/pull/10021), we'll need an official release. I've opened up an issue on GitHub ( https://github.com/cctbx/cctbx_project/issues/451). Please provide any feedback on the versioning system, release schedule, and anything release related. Let us know if you're scripts are not working with these packages. Thanks! -- 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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Generating electron density from protein coordinate (PDB)
by Kit Sang Chu 19 Mar '20

19 Mar '20

Dear phenix users, Although phenix in general is used to convert electron density into protein coordinates (PDB), I am interested in retrieving electron density of an optimized PDB, hopefully at a resolution of ~1-2A. Since there could be manipulation of the coordinate file upstream, some crystal structure information could be lost. I notice that phenix generates structure factor from coordinates (assuming P1 symmetry) by phenix.fmodel. However, the conversion from structure factor to electron density requires a normalization constant (sum of atomic form factors). I am still trying to identify the correct function to use to output a non-binary output format. phenix.maps might work but I am unsure about the map_type. If anyone is willing to provide some suggestions, that would be very helpful. Sincerely, Simon

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Re: [phenixbb] Transferring Phenix home
by Engin Özkan 19 Mar '20

19 Mar '20

There is an Import Project function in the Projects pull-down menu (on a Mac; don't know where that would be in linux/Windows). If you copy your entire project folder, including the .phenix subfolder, to a second computer, you can import the project using the Import Project function, and the project will be added to your current list of projects on the second computer. Used to work well several years ago, probably still works well. Engin On 3/18/20 4:36 PM, Boaz Shaanan wrote: > Hi, I have done this (moving phenix stuff between computers) a few > times on linux os (ubuntu's versions). Just backup your whole > phenix-projects directory on your computer (from the top down to all > the sub-dirs) and dump it onto the new computer. Your projects will > show up in the gui, don't worry. > It worked for me. > Stay safe. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Mar 18, 2020 23:23, csteussy <csteussy(a)purdue.edu> wrote: > All, > > In this age of self quarantine I have moved a number of my PHENIX > projects home. All the working subdirectories have a .phenix entry. Is > there a way to incorporate the history of the projects from work to my > home installation. Starting the GUI shows none of it. > > Both of these are Ubuntu 18.04 and I have sudo privileges. > > Thanks in advance. > > Nic out > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > _______________________________________________ > 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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Raw diffraction images for SARS-CoV-2 related structures
by Gerard Bricogne 18 Mar '20

18 Mar '20

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.

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Transferring Phenix home
by csteussy 18 Mar '20

18 Mar '20

All, In this age of self quarantine I have moved a number of my PHENIX projects home. All the working subdirectories have a .phenix entry. Is there a way to incorporate the history of the projects from work to my home installation. Starting the GUI shows none of it. Both of these are Ubuntu 18.04 and I have sudo privileges. Thanks in advance. Nic out

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COVID-19 Structural Biology Data Analysis
by Paul Adams 18 Mar '20

18 Mar '20

Dear Colleagues, with the effects of COVID-19 being felt worldwide, we all want to do something to help. There are several teams that are using crystallography and cryo-EM to help develop diagnostics and therapeutics for the virus. We wanted to let you know that the members of the Phenix team stand ready to assist with the analysis of COVID-19 related data should that be helpful to you. Please feel free to contact any of us. We hope that you are able to stay safe in this very challenging time. Paul, on behalf of the Phenix Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. [repost]
by Bjørn Panyella Pedersen 18 Mar '20

18 Mar '20

Dear colleagues, 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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Slurm/qsub queue usage
by Michael Weyand 18 Mar '20

18 Mar '20

Dear Phenixer, I would like to use Phenix GUI queue execution option. We have access to cluster nodes via Slurm/qsub. https://slurm.schedmd.com/documentation.html The reason is that we have severe problems to run Coot/PyMol form the Phenix GUI if Phenix is executed on our number cruncher. This direct Coot usage GUI option is HIGHLY preferred by my young colleagues... Therefore my Slurm queue installation. But I have no clue how to add the needed first qsub script line ( "#!/bin/bash" or "#!/bin/tcsh" ) to the final Phenix command script from the Phenix GUI, which is to my knowledge a must for the qsub/sbatch command. Same holds true for the CCP4i GUI ... :-( This line is added to avoid cross positing to CCP4BB ... ;-) Is there any simple hint / command which I have missed ? Kind regards, Michael

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exit code 126
by Wim Burmeister 18 Mar '20

18 Mar '20

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crash when running PDB Tools job in 1.18rc4
by Daniel Larsson 18 Mar '20

18 Mar '20

Just want to report a bug in the latest release candidate. I just installed it and when I try to open an old PDB Tools job or start a new one, the GUI crashes without any error message. The same thing works fine with 1.18rc1. I’m using macOS 10.14.6 (Mojave). Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Fwd: prepare_pdb_deposition produce incomplete results in version 1.17
by Billy Poon 13 Mar '20

13 Mar '20

-- 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 ---------- Forwarded message --------- From: Billy Poon <BKPoon(a)lbl.gov> Date: Wed, Mar 11, 2020 at 11:51 PM Subject: Re: [phenixbb] prepare_pdb_deposition produce incomplete results in version 1.17 To: Marta Martinez <mmmtnez(a)cnb.csic.es> Hi Marta, The mmCIF functionality is very much still a work in progress as we try to make the process more robust. The ? in the column from 1.17 is a consequence of some changes we had made to the code and we're working on fixing that. The secondary structure issue with Chimera is separate since that column is for matching the protein chain with the sequence, not as a way to annotate secondary structure. We are working with the wwPDB to make sure our output is in compliance with the latest mmCIF dictionary. Let us know if you have any other questions. Thanks! -- 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 On Mon, Mar 9, 2020 at 10:05 AM Marta Martinez <mmmtnez(a)cnb.csic.es> wrote: > > Hi, > > In the past (phenix version 1.13) we have been using > prepare_pdb_deposition to generate CIF files of atomic structures. In > the last version (1.17) the program produces an incomplete output if > the input is a PDB file. > > The tests have been carried out with the protein hemoglobin (PDB > ID = 5ni1). If we downloaded it from the PDB databank we get the file > 5ni1.cif. If we "export" 5ci1.cif using prepare_pdb_deposition the > result is correct. On the other hand, if we convert 5ci1.cif to PDB > either using chimera uscf or maxit > (https://sw-tools.rcsb.org/apps/MAXIT/index.html) and then we execute > prepare_pdb_deposition, one of the columns (label name = > _atom_site.label_entity_id) is filled with the symbol "?" instead of > the label_entity_id (as the version 1.13 did). One of the effects of > this misbehavior is that chimera displays the file as a set of > aminoacids with no connection between them (no secondary structure is > shown) > > > > A few lines of the file obtained using phenix 1.17: > > ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A ? > 1 1 > ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A > ? 1 1 > ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A ? > 1 1 > > Corresponding lines of the equivalent file obtained using phenix 1.13 > > ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A 1 > 1 1 > ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A > 1 1 1 > ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A 1 > 1 1 > > Note the difference in the ante-penultimate column. > > We would appreciate if phenix 1.17 is modified so the column > _atom_site.label_entity_id is filled with the proper chain ID. > > best wishes > > -- > Marta Martinez Gonzalez > > Biocomputing Unit (Lab B13) > National Center for Biotechnology-CSIC > Darwin, 3. Campus de la Universidad Autonoma de Madrid > 28049 Madrid. Spain > Tel:+34 915854510 Fax:+34 913720112 > E-mail: mmmtnez(a)cnb.csic.es > > _______________________________________________ > 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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phenix.geometry_minimization with amber option
by Wei Wang 12 Mar '20

12 Mar '20

Dear all, I try to use phenix.geometry_minimization with amber option, but when reaching minimization step, the function always crash. If I don’t use amber option, then it’s ok. The commands I put in was like: phenix.geometry_minimization 4phenix_xyz.pdb amber.use_amber=true amber.topology_file_name=4amber_xyz.prmtop amber.coordinate_file_name=4amber_xyz.rst7 amber.order_file_name=4amber_xyz.order I tried both 1.17 stable and latest overnight build. Please share your advice, thx! Wei

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prepare_pdb_deposition produce incomplete results in version 1.17
by Marta Martinez 09 Mar '20

09 Mar '20

Hi, In the past (phenix version 1.13) we have been using prepare_pdb_deposition to generate CIF files of atomic structures. In the last version (1.17) the program produces an incomplete output if the input is a PDB file. The tests have been carried out with the protein hemoglobin (PDB ID = 5ni1). If we downloaded it from the PDB databank we get the file 5ni1.cif. If we "export" 5ci1.cif using prepare_pdb_deposition the result is correct. On the other hand, if we convert 5ci1.cif to PDB either using chimera uscf or maxit (https://sw-tools.rcsb.org/apps/MAXIT/index.html) and then we execute prepare_pdb_deposition, one of the columns (label name = _atom_site.label_entity_id) is filled with the symbol "?" instead of the label_entity_id (as the version 1.13 did). One of the effects of this misbehavior is that chimera displays the file as a set of aminoacids with no connection between them (no secondary structure is shown) A few lines of the file obtained using phenix 1.17: ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A ? 1 1 ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A ? 1 1 ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A ? 1 1 Corresponding lines of the equivalent file obtained using phenix 1.13 ATOM 1 N . VAL A 1 ? 45.71600 55.72700 67.16700 1.000 80.64000 N ? A 1 1 1 ATOM 2 CA . VAL A 1 ? 46.41500 54.48900 67.60900 1.000 80.57000 C ? A 1 1 1 ATOM 3 C . VAL A 1 ? 45.42800 53.30800 67.68900 1.000 75.67000 C ? A 1 1 1 Note the difference in the ante-penultimate column. We would appreciate if phenix 1.17 is modified so the column _atom_site.label_entity_id is filled with the proper chain ID. best wishes -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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Postdoc position, Sugar Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 04 Mar '20

04 Mar '20

Dear colleagues, Please pass this along to anyone 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 Apr. 2nd, 2020.

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