- phenixbb - phenix-online.org

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 20 Mar '20

20 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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