- phenixbb - phenix-online.org

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

2 1

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

1 1

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

2 4

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

2 1

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.

1 0

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

1 0

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 ] --

1 0

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.

1 0

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

2 1

exit code 126
by Wim Burmeister 18 Mar '20

18 Mar '20

2 1

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

2 1

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 >

2 1

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

2 1

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

1 0

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.

1 0

Real-space refinement fails to restrain CYS SG ZN properly
by Aaron Oakley 03 Mar '20

03 Mar '20

I'm trying to refine a structure containing ZN bound to four cysteine residues. I have had trouble with Real-space refinement mangling the residues around this ZN. At first, Real-space refinement tried to turn the cysteine into disulfides. I tried switching this off with… resname CYS and name SG …in the disulphide bond exclusion selection string under the Model interpretation menu (there are no disulfides in the protein). But the cysteine-zinc cluster continued to be mangled. Inspection of the .geo file shows that the SG-ZN distance is being restrained, but the CB–SG–ZN angle is not. I checked the relevant dictionary file... phenix-1.17.1-3660/modules/chem_data/mon_lib/list/mon_lib_list.cif And the correct bond and angle restraints do seem to be present: . . . ZN-CYS 1 ZN 2 SG single 2.340 0.020 . . . ZN-CYS 1 ZN 2 SG 2 CB 109.000 3.000 . . . Suggestions on how to fix this welcome. –å

3 2

Dock in map fails with search map file.
by Aaron Oakley 28 Feb '20

28 Feb '20

Salvete! I am trying to use Dock in map to superimpose one map onto another. The job runs, but fails with PHENIX error: “Job294_sharpened_relion.mrc_as_model_refine_001.pdb" is not a known model type. Inspection of this file suggests that it is indeed a proper PDB file. (The original map I am trying to move is job294_sharpened_relion.mrc). Any solutions? Thanks, –å

1 0

real space correlation coefficient from the command line
by Daniel Larsson 25 Feb '20

25 Feb '20

Hi, When running a real-space refine, there is an option in the results to save a text file with real-space correlation coefficients (correlation_coeficients.txt). Is there a way to calculate these numbers from the command line? It would save me a lot of clicking, sinceI have dozens of maps which I want to run in parallel and analyze using scripts. 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

2 1

IUCr2020 Computing School in Nove Hrady - 17th to 22nd August - Registration opened
by Claudia Millán Nebot 24 Feb '20

24 Feb '20

Dear all, We announce the IUCr Computing School in Nove Hrady (Czech Republic) which will take place between 17th and 22nd August 2020 prior to the IUCr Congress in Prague. Registration has already started. Further information about the school can be found on the website: https://www.xray.cz/iucr/workshops/nh/default.htm. Follow also our hashtag on Twitter, #IUCr2020CompSchool. Active developers of crystallographic software, tools and methods are invited to participate at this Computing School. The school is not introductory and it is recommended that participants already have some basic programming skills and crystallographic knowledge. Our aim is to discuss and exchange ideas and to tackle the challenges related to the method development in crystallography. Participants can be early-career scientists (PhD students, Postdocs, etc.) as well as established developers. Our confirmed speakers are: - Simon Billinge (Columbia University, USA) - Luc Bourhis (Bruker, France) - Paul Boyle (Western University, London, Ontario, Canada) - Iracema Caballero (Institut de Biologia Molecular de Barcelona, Spain) - Gemma de la Flor (Karlsruhe Institute of Technology, Germany) - Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) - Rafiga Masmaliyeva (Institute of Molecular Biology and Biotechnology, Azerbaijan) - Garib Murshudov (Laboratory of Molecular Biology-MRC, UK) - Reinhard Neder (Institute of Condensed Matter Physics, Erlangen, Germany) - Alexandre Ourjoumtsev (Institut de Génétique et de Biologie Moléculaire et Cellulaire, France) - Randy Read (University of Cambridge, UK) - Massimo Sammito (University of Cambridge, UK) - Arkadiy Simonov (Eidgenössische Technische Hochschule Zürich, Switzerland) - Melanie Vollmar (Diamond Light Source Ltd, Harwell Science & Innovation Campus, United Kingdom) - Thomas White (Center for Free-Electron Laser Science, Hamburg, Germany) For any questions regarding the school please contact us. Best wishes, Claudia Millán (cmncri at ibmb.csic.es) Martin Lutz (m.lutz at uu.nl) Jan Rohlicek (rohlicek at fzu.cz) PD. Please find attached a poster about the school that you can forward, together with this email, to people potentially interested in participating in the Computing School. ---------------------------------------------------------------------------------------- Claudia Millán (cmncri(a)ibmb.csic.es) Crystallographic Methods Group http://chango.ibmb.csic.es Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain LinkedIn: es.linkedin.com/in/claudiamillan/ <http://es.linkedin.com/pub/claudia-mill%C3%A1n/60/a76/821/> ResearchGate: https://www.researchgate.net/profile/Claudia_Millan?ev=hdr_xprf Twitter: https://twitter.com/cheshireminima

1 1

Berkeley Lab Exascale Computational Crystallographer
by Nicholas Sauter 19 Feb '20

19 Feb '20

Discover your future at Berkeley Lab! Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging Division ( https://biosciences.lbl.gov/divisions/mbib/) has an opening for an Exascale Computational Crystallographer Project Scientist. The Project Scientist, with a strong interest in high-performance computing and an intuitive feel for experimental data, will be affiliated with the Exascale Computing Project, specifically Nick Sauter’s Data Analytics for X-ray Free Electron Lasers (XFELs) group focusing on scientific software for X-ray crystallography. The next decade of structural biology at the Linac Coherent Light Source (LCLS) will include groundbreaking advances in time-domain crystallography, performed at room temperature to preserve biologically relevant dynamic mechanisms. Considering the anticipated scale of these datasets, we have an ambitious collaboration between SLAC, LANL, and LBNL to utilize national supercomputer facilities for near real-time analysis, in close collaboration with scientists at NERSC (also located in Berkeley). The group’s projects will include: • Photosystem II, discovering the sequence of redox events leading to the release of molecular oxygen, using a combination of time-resolved crystallography and X-ray emission spectroscopy. https://doi.org/10.1038/s41586-018-0681-2 • Examining the electronic environment of metalloenzyme catalytic metals, with detection based on anomalous scattering. The Project Scientist will be positioned to launch into high-performance computing careers at a light source or other experimental facilities. https://doi.org/10.1107/S2059798320000418 Please have a look at our job posting at https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=89727 Nicholas K. Sauter, Ph. D. Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720 (510) 486-5713

1 0

Macromolecular Crystallography School, Madrid 2020 (MCS2020)
by Armando Albert 19 Feb '20

19 Feb '20

Dear colleagues, We are pleased to announce the 10th edition of the Macromolecular Crystallography School 2020, to be held at the Institute Química-Física Rocasolano- CSIC (Madrid, Spain). Dates: April 13 - 18, 2020 The workshop has been designed for postgraduate, postdoctoral and research scientists that deal with macromolecular crystallography and cryo EM but need further knowledge on the routine uses, the state of the art and fundamentals that underlie the modern techniques for macromolecular crystallography and cryo EM. The topics will cover crystallographic computing and fundamentals using XDS, CCP4 and Phenix, as well as the state of the art on topics such as the strategies for protein production, data collection, phasing, automated pipelines at synchrotron and refinement with ARCIMBOLDO, SHELX and SIR2014 and modeling with COOT. MCS2020 will provide six days of lectures and workshops. The course is designed for 25 highly motivated attendants. Requests to participate must be sent by a free-formated E-mail, before March 11th, 2020 to the following address: cursos(a)fgua.es <mailto:[email protected]>, indicating the motivation to participate and experience on macromolecular crystallography and including a letter of recommendation from PhD Director (only for PhD students). Invited speakers and tutors: - Maria Solá, Barcelona, Spain - Isabel Usón, Barcelona, Spain - Paul Adams, Berkeley, USA - Pavel Afonine, Berkeley, USA - Kay Diederichs, Konstanz, Germany - Paul Emsley, Cambridge, UK - Rafael Fernández-Leiro, Madrid, Spain - Carmelo Giacovazzo, Bari, Italy - Eugene Krissinel, Oxford, UK - Jose. A. Marquez, Grenoble, France - Claudia Millan, Barcelona, Spain - Begoña Monterroso, Madrid, Spain - Rob Nicholls, Cambridge, UK - Santosh Panjikar, Australia - Carmen San Martín, Madrid, Spain Please find attached the program of the Workshop, the application form and further information at http://www.xtal.iqfr.csic.es/MCS2020/ <http://www.xtal.iqfr.csic.es/MCS2020/> Organizers: Armando Albert (xalbert(a)iqfr.csic.es <mailto:[email protected]> ), Juan A. Hermoso (xjuan(a)iqfr.csic.es <mailto:[email protected]>) and Isabel Usón (iufcri(a)ibmb.csic.es <mailto:[email protected]>)

1 0

EMBO meeting on “Molecular Neurobiology” 8-12 May 2020
by Janssen, B.J.C. (Bert) 17 Feb '20

17 Feb '20

Dear all, We would like to draw your attention to the EMBO workshop on "Molecular Neurobiology", taking place on the beautiful island of Crete on 8-12 May 2020. The meeting brings together world leading scientists, group leaders and young researchers with a keen interest in the latest science occurring at the interfaces of structural biology, biophysics, molecular & cellular imaging and neuroscience. Given its cross-disciplinary nature, the meeting presents a broad overview of molecular neurobiology, ample opportunities for discussions and a sneak peek into the latest developments. See http://meetings.embo.org/event/20-molneuro for more information and application guidelines, registration deadline is 15 Feb. 2020. Organizers: Alain Chédotal, Institut de la Vision, France Bert Janssen, Utrecht University, the Netherlands Chenghua Gu, Harvard University, USA Elena Seiradake, University of Oxford, UK Nektarios Tavernarakis, IMBB FORTH, Greece Best wishes Bert Bert Janssen Bijvoet Center for biomolecular research Utrecht University Padualaan 8, 3584 CH, Utrecht

1 1

PhD position available
by Tobias Beck 17 Feb '20

17 Feb '20

Dear all, There is an opening for a PhD position in my group. The Beck group recently moved to Hamburg, where we have labs well-equipped for chemistry, biochemistry and molecular biology. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. The project involves protein redesign, protein chemistry and characterization and more. The post is available immediately / upon arrangement. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/… The group homepage can be found here: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html Deadline for applications is March 15 2020. Please contact me for further information or informal inquiries: tobias.beck @chemie.uni-hamburg.de Best, Tobias. ____________________________________________________________ Prof. Dr. Tobias Beck University of Hamburg Department of Chemistry Institute of Physical Chemistry Grindelallee 117 D-20146 Hamburg Germany phone: +49 4042838 8210 fax: +49 4042838 3462 web: www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/ ____________________________________________________________

1 0

Job Posting: Surrozen Inc., RA / SRA - Biophysics / Biochemistry
by Parthasarathy Sampathkumar 15 Feb '20

15 Feb '20

Dear All, Please allow me to post this link for RA / SRA - Biophysics / Biochemistry Position at Surrozen with focus on Antibody Developability and Structural Biology. https://apply.workable.com/surrozen/j/75748FA62D/ I request interested job seekers to apply directly online using the above link. Thanks, Best Wishes, Partha __________________________ Parthasarathy Sampathkumar PhD Senior Scientist, Surrozen Inc., 171 Oyster Point Blvd., Suite 400 South San Francisco, CA 94080 Email: partha(a)surrozen.com

1 0

Neutrons in the Environment and Life Sciences Workshop - HANDS 2020
by Meilleur, Flora 13 Feb '20

13 Feb '20

First announcement HANDS 2020 HFIR/SNS Advanced Neutron Diffraction and Scattering Workshop Oak Ridge, TN. June 1 - June 5, 2020 Oak Ridge National Laboratory, in conjunction with North Carolina State University, and support from the National Science Foundation and the Shull Wollan Center - a Joint Institute for Neutron Scattering, celebrates a decade of neutron scattering education in structural biology at ORNL with the HFIR/SNS Advanced Neutron Diffraction and Scattering workshop (HANDS 2020). Detailed information can be found on the workshop web page: https://conference.sns.gov/event/217/. Application deadline: April 24, 2020 Fellowships to support travel and accommodation are available (subject to availability of funds) The workshop aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Participants of HANDS 2020 will become familiar with neutron techniques with hands-on experiments in sample preparation, crystallography, small angle scattering, reflectometry and neutron spin echo. The workshop is designed for graduate students, post-doctoral fellows and faculty with limited to no experience with neutron sciences. Flora Meilleur, Ph. D Neutron Scattering Scientist, Neutron Scattering Division Oak Ridge National Laboratory Associate Professor, Molecular and Structural Biochemistry North Carolina State University

1 0