Re: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others
Hi, SHARP and autoSHARP are manually run using the Sushi interface, which is not the easiest thing to set up. For straightforward heavy atom refinement, you can run both SHARP and autoSHARP on the command line. If you are familiar with SHARP’s input files and parameters, instructions can be found here: https://www.globalphasing.com/sharp/manual/appendix2.html However, if you need to do more difficult refinement and require more manual control over the SHARP parameters, the Sushi interface is vastly preferred. If you are new to SHARP and just want to try it out on a dataset without manual intervention, the easiest way to do this is to use run_autoSHARP, a command line script that automates nearly all the setup. You supply a dataset, sequence, and a heavy atom list (optional, if you don’t have one, it will run SHELXD for you). Instructions here: https://www.globalphasing.com/sharp/wiki/index.cgi?RunAutoSharp You can also run autoSHARP via CCP4, if you link your installation to it. Best, Aaron From: CCP4 bulletin board on behalf of fuxingke Reply-To: fuxingke Date: Wednesday, October 11, 2023 at 12:02 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Refinement of heavy atoms using SOLVE or SHARP or others Dear Colleagues, Reacently, for SAD experiment, I find SOLVE and SHARP can refine the variables of heavy atoms, such as occupancies, coordinates and thermal parameters. But how to use SOLVE and SHARP to refine heavy atom in command line in linux? I don't find a script to do it. Who has the scripts template that implements the refinement of heavy atoms using SOLVE or SHARP or others? Could you please share them with me? Regards Best wishes, Fu Xingke Institute of Physics CAS To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] PyMol tutorials: Summary
Hi all, I’ll add to this list the videos by Pymol Ross- I particularly like his videos because he shows how to do things via both the GUI and the command line: https://www.youtube.com/@pymolross Best, Aaron -- Aaron Finke Beamline Scientist, MAX IV Lund University e-mail: aaron.fi...@maxiv.lu.se<mailto:aaron.fi...@maxiv.lu.se> On Aug 4, 2023, at 18:08, Patrick Loll mailto:pjl...@gmail.com>> wrote: Thanks to everyone who responded to my query about PyMol tutorials. Several people evinced interest in seeing a summary of the results, so I’m attaching one below: YouTube tutorials for PyMol: = 1) Molecular Memory got a number of mentions: https://www.youtube.com/@MolecularMemory/videos: e.g. PyMol 101, lessons 1 & 2 2) Another recommended source was the bumbling biochemist site: https://youtube.com/@thebumblingbiochemist (e.g., https://www.youtube.com/watch?v=GpxCGQAhgi8=15s) 3) Keni Vidilaseris has assembled a number of tutorials here: https://youtube.com/playlist?list=PLfdvnKKZWSxCBL8uDQuc9bAttmAg3-_LS 4) Here are a couple of videos recommended by Mitch Miller: https://www.youtube.com/watch?v=h5wKppcyzOw & https://guides.lib.vt.edu/c.php?g=947485 5) Here’s a link recommended by Amit Bablekar: https://www.youtube.com/watch?v=h5wKppcyzOw 6) And for cranky oldsters such as myself, here’s an actual document: https://dasher.wustl.edu/bio5357/software/pymol/simple-tutorial.pdf 7) Finally, John Hasty also pointed out that there is a Google Colab notebook with various PyMol scripts. Much obliged for the help! Pat --- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Crystallisation textbook
I second the Acta F special issue (as an unbiased reviewer): https://journals.iucr.org/special_issues/2016/crystallization/ Best, Aaron -- Aaron D. Finke, PhD Staff Scientist, MAX IV Laboratory e-mail: aaron.fi...@maxiv.lu.se On Jul 14, 2023, at 17:19, Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> wrote: Hi all, I'd be grateful for any recommendations of a good up-to-date textbook covering macromolecular crystallisation. Currently we are using the excellent book by Terese Bergfors (2009) but would be interested if there is anything more recent with discussion around automation, micro-crystallisation and so on Many thanks in advance for your help! Kind regards, Mike -- 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 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] checkCIF alert
Hi Soheil, This usually means there are outliers in the reflection list that are affecting the weight parameter S that SHELXL uses. Use the OMIT instruction in your SHELXL .ins file to remove those ten disagreeable reflections, e.g. OMIT -1 -1 1 OMIT 1 0 1 etc. In addition, this tends to include low-angle reflections measured “behind” the beamstop. In your CheckCIF you may have an PLAT919_ALERT that checks for such reflections. Best, Aaron -- Aaron Finke Beamline Scientist, MAX IV Lund University e-mail: aaron.fi...@maxiv.lu.se<mailto:aaron.fi...@maxiv.lu.se> On Jun 12, 2023, at 09:51, Soheil Mahmoudi mailto:soheil.mahmo...@univie.ac.at>> wrote: Hi Everyone, I am preparing a cif file from an inorganic compound measured with X-ray, I get an unexpected error during chechCIF evaluation as below, Alert level A,PLAT939_ALERT_3_A Large Value of Not (SHELXL) Weight Optimized S .1029.36 Check I check the disagreeable reflection and there is no more than 10. Please let me know how I can solve or justify this error if you have already encountered such a problem. Best Regards -- Soheil Mahmoudi MSc, Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, 1090 Wien To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] checkCIF alert
Hi Soheil, This usually means there are outliers in the reflection list that are affecting the weight parameter S that SHELXL uses. Use the OMIT instruction in your SHELXL .ins file to remove those ten disagreeable reflections, e.g. OMIT -1 -1 1 OMIT 1 0 1 etc. In addition, this tends to include low-angle reflections measured “behind” the beamstop. In your CheckCIF you may have an PLAT919_ALERT that checks for such reflections. Best, Aaron -- Aaron Finke Beamline Scientist, MAX IV Lund University e-mail: aaron.fi...@maxiv.lu.se<mailto:aaron.fi...@maxiv.lu.se> On Jun 12, 2023, at 09:51, Soheil Mahmoudi mailto:soheil.mahmo...@univie.ac.at>> wrote: Hi Everyone, I am preparing a cif file from an inorganic compound measured with X-ray, I get an unexpected error during chechCIF evaluation as below, Alert level A,PLAT939_ALERT_3_A Large Value of Not (SHELXL) Weight Optimized S .1029.36 Check I check the disagreeable reflection and there is no more than 10. Please let me know how I can solve or justify this error if you have already encountered such a problem. Best Regards -- Soheil Mahmoudi MSc, Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 42, 1090 Wien To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] REMINDER:
Dear all, On Sept 30 & Oct 1, 2021, the Cornell High Energy Synchrotron Source will host an online workshop identifying forefront research questions probing applications and consequences of macromolecular crystallography under ambient (room temperature to physiological) conditions. A secondary lens will be experimental methods that support this research, including both synchrotron-based and complementary tools. Registration is free. Registration and additional workshop information can be found here<https://www.chess.cornell.edu/ambient-crystallography-chess-2030-workshop>. We sincerely hope you will join us. Please reach out to the CHESS Users Office<mailto:chessuseroff...@cornell.edu> or Aaron Finke with any questions or for further details. Warm regards, Aaron Finke and Daniel Keedy, organizers ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Prof. Jack Dunitz, 1923-2021
Dear all, It is with a heavy heart that I announce the passing of Prof. Jack Dunitz at the age of 98. Prof. Dunitz was a giant in the development of modern crystallographic methods, most notably in the determination of the crystal structure of ferrocene, confirming the “sandwich complex” nature of that molecule and ushering in the field of organometallic chemistry. As a crystallographer, mathematician, and chemist, Prof. Dunitz effectively bridged the gap between crystallography and chemistry, inspiring chemists to exploit the utility of the burgeoning field of crystallography. He was a professor at ETH-Zurich for over 60 years, and even after his “retirement” in 1990, dedicated his life to crystallographic research. I have many fond memories of Prof. Dunitz from my time at ETH. Even at the age of 91, he still came into the office at least three times a week to pursue research programs; I am told he continued to come in regularly until Covid forced the campus closed. His wit and curiosity never dulled, and was enamored with new technologies that enabled various new forms of crystallographic research. He owned an iPad before I ever did! As a postdoc doing crystallography, Prof. Dunitz enjoyed calling me into his office, ostensibly to help him use some feature of CCDC Mercury, but in reality to discuss some new idea he had about crystal symmetry and exploiting it to gain some greater understanding of coordination complexes. He was the kind of person who had forgotten more chemistry than I will ever know, and these discussions were always enlightening and entertaining, mixing new theory with the history of crystallography, much of which he bore witness or contributed to. He will be sorely missed. If you would like to express your condolences, please use the following email address: jack_condole...@ethz.ch<mailto:jack_condole...@ethz.ch> Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] CHESS Ambient Crystallography Workshop, Sept 30-Oct 1, 2021
Dear all, On Sept 30 & Oct 1, 2021, the Cornell High Energy Synchrotron Source will host an online workshop identifying forefront research questions probing applications and consequences of macromolecular crystallography under ambient (room temperature to physiological) conditions. A secondary lens will be experimental methods that support this research, including both synchrotron-based and complementary tools. Registration is free. Registration and additional workshop information can be found here<https://www.chess.cornell.edu/ambient-crystallography-chess-2030-workshop>. We sincerely hope you will join us. Please reach out to the CHESS Users Office<mailto:chessuseroff...@cornell.edu> or Aaron Finke with any questions or for further details. Warm regards, Aaron Finke and Daniel Keedy, organizers ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoctoral Associate Position at CHESS, Cornell University
The Macromolecular Diffraction and High Pressure Biology resources at the Cornell High Energy Synchrotron Source (MacCHESS and CHEXS/HP-Bio, respectively) have an opening for a Postdoctoral Associate to develop applications of high pressure to answer biological questions concerning enzyme mechanisms, protein folding, adaptation to extreme environments, and the origin of life. The primary method to be used is pressurization of macromolecular crystals in a diamond anvil cell (HP-MX), but other techniques such as high-pressure small angle X-ray scattering (HP-SAXS) will also be available. A Ph.D. degree in structural biology, biophysics, or a related field is required. Experience in crystallography is highly desirable, and experience working with samples in "non-standard" environments is a plus. The ability to identify suitable systems for study, through researching previous work and establishing suitable collaborations, is essential. In addition to pursuing his/her own study of pressure effects, the successful candidate will be expected to assist research groups seeking to use high-pressure techniques at CHESS for their work. Please apply for the position here: https://academicjobsonline.org/ajo/jobs/18189 For more information about the position, please contact myself or Marian Szebenyi (dm...@cornell.edu<mailto:dm...@cornell.edu>). ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Beam Time for Macromolecular Crystallography at CHESS: Spring 2021 Proposals due TODAY!
Dear CCP4BB Members, The new and fully-upgraded macromolecular crystallography beamline at CHESS, FlexX, is now accepting proposals for the Spring 2021 run. SPRING 2021 RUN: The regular proposal deadline for the Spring 2021 run is TODAY, Nov. 19, 2020. However, we will accept late proposals due to Covid, but please submit as soon as possible to secure beamtime! The FlexX station (beamline ID7B2) is the all-new macromolecular crystallography station at CHESS. The recently completed CHESS upgrade has considerably improved our capabilities in order to meet the the stringent demands of users. Current capabilities include: * undulator source with multilayer monochromator for high flux. 7-14 keV energy range. Standard beam sizes available: 100 x 100 um (H x V FWHM) and 10 x 10 um microbeam. * single-axis goniostat, EIGER2 16M detector, BAM2 automounter accepting Unipucks * remote data collection with on-site CHESS staff scientist support (NB: due to Covid and occupancy restrictions, physical access for users to CHESS is very limited, so remote data collection is highly recommended!) * we welcome "non-standard" experiments! The staff at CHESS is more than happy to work with users who want to perform experiments beyond standard rotation cryocrystallography. Interested in trying serial crystallography for room-temperature data collection, or microcrystals? High-pressure cryocooling for reduced mosaicity? High-pressure crystallography with a diamond anvil cell? We can accommodate your needs and more! Interested? Instructions for submitting a proposal here: https://www.chess.cornell.edu/users/new-user-guide Feel free to contact me with any questions! Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Beam Time for Macromolecular Crystallography at CHESS: Now Accepting Spring 2021 Proposals
Dear CCP4BB Members, The new and fully-upgraded macromolecular crystallography beamline at CHESS, FlexX, is now accepting proposals for the Spring 2021 run. SPRING 2021 RUN: The regular proposal deadline for the Spring 2021 run is Oct. 28, 2020. However, we will accept late proposals due to Covid, but please submit as soon as possible to secure beamtime! The FlexX station (beamline ID7B2) is the all-new macromolecular crystallography station at CHESS. The recently completed CHESS upgrade has considerably improved our capabilities in order to meet the the stringent demands of users. Current capabilities include: * undulator source with multilayer monochromator for high flux. 7-14 keV energy range. Standard beam sizes available: 100 x 100 um (H x V FWHM) and 10 x 10 um microbeam. * single-axis goniostat, EIGER2 16M detector, BAM2 automounter accepting Unipucks * remote data collection with on-site CHESS staff scientist support (NB: due to Covid and occupancy restrictions, physical access for users to CHESS is very limited, so remote data collection is highly recommended!) * we welcome "non-standard" experiments! The staff at CHESS is more than happy to work with users who want to perform experiments beyond standard rotation cryocrystallography. Interested in trying serial crystallography for room-temperature data collection, or microcrystals? High-pressure cryocooling for reduced mosaicity? High-pressure crystallography with a diamond anvil cell? We can accommodate your needs and more! Interested? Instructions for submitting a proposal here: https://www.chess.cornell.edu/users/new-user-guide Feel free to contact me with any questions! Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Pointless with fast close?
I’m running Pointless on a large number of datasets, just to search for higher symmetry (the only options I’m inputting are xdsin XDS_ASCII.HKL and SETTING SYMMETRY-BASED). I’ve noticed that after the symmetry search, it pauses for a few seconds after the “Filename:” output, then ends normally with the pointless references. I don’t know why it’s doing that and it’s making a batch run of pointless much longer than it should be. Any suggestions? Thanks, Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery
Yes, this issue will definitely compete with IUCr's many journals dedicated to kinase drug discovery. /sarcasm On a more serious note: nobody should be "loyal" to a journal or scientific society; both are servants of the scientific community, not the other way around. If they stop supporting scientists with their roles and policies, those scientists will move elsewhere (note, for example, the American Crystallographic Association and the diaspora of structural biologists/protein crystallographers from the ACA). If I submit to an IUCr journal, it is because my work is geared toward the community of IUCr journal readers. IUCr journals are not always going to attract the right audience for a particular study, and that's fine. Not everyone here is a capital-C Crystallographer, and if someone in this community wants to bring to our attention an opportunity that may benefit its users, that's great! I take issue with MDPI's policies as a publishing house, but guest editors posting about a special issue on behalf of them is more beneifical than harmful. In that vein, advertistments for job postings are professionally-related and also not relevant to CCP4 but I think everyone, especially young scientists, benefit from those as well. Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Nov 22, 2019, at 8:58 AM, Isabel Uson mailto:iuf...@ibmb.csic.es>> wrote: Dear Julie and Mathew, I feel advertisement on behalf of professional publishers is not appropriate for the bulletin board. MDPI should pay for its advertisements, rather than get them for free. (Being a for-profit firm, they should also pay for, rather than invite editing, but this is of course personal). They stand in direct competition with IUCr journals, which it should be in our best interest to protect. We all profit from constant -rather than occasional- scientific editing and the IUCr support to our community (meetings, fellowships, awards). I know it is not the first time such a call is posted in the bb and that it is not for me to say what is appropriate or not but I will really miss journals from our scientific societies the day they become extinct. Best wishes, Isabel On Thu, Nov 21, 2019 at 1:07 AM CCP4BB automatic digest system mailto:lists...@jiscmail.ac.uk>> wrote: There are 2 messages totaling 363 lines in this issue. -- Date:Wed, 20 Nov 2019 17:24:15 + From:Julie Tucker mailto:julie.tuc...@york.ac.uk>> Subject: Off-topic (somewhat): Call for papers on structure-guided kinase drug discovery Dear colleagues, Mathew Martin and I would very much appreciate your contributions on the topic of "Recent Advances in Structure-Guided Kinase Drug Discovery" for a special issue of the International Journal of Molecular Sciences <http://www.mdpi.com/journal/ijms> (IJMS, ISSN 1422-0067, Current Impact Factor: 4.183). We encourage submission of both *original research articles and topical reviews* on all aspects of *structure-guided drug discovery targeting the phosphotransferase enzyme family*. We welcome accounts of your experiences of applying structure-guided methods of all types to the discovery and development of inhibitors of protein, lipid and small molecule kinases from bacteria to man. More information can be found here: https://www.mdpi.com/journal/ijms/special_issues/structure_guided_kinase. Due to its open access policy, the journal charges publication fees, however, please contact us directly for the chance to secure a discount on the usual fee. The deadline for submissions is nominally 20th April 2020, however, articles will be peer-reviewed and published on an ongoing basis. Our apologies to those of you with no interest in kinase drug discovery, and our heartfelt thanks to any of you who feel moved to contact us to discuss potential contributions. Please also feel free to pass this invitation on to any interested colleagues. Best wishes, Julie Tucker and Mathew Martin -- Julie Tucker York Biomedical Research Institute Department of Biology and HYMS University of York Heslington YORK YO10 5DD Tel. 01904 328912 Co-guest editor of "Recent Advances in Structure-Guided Kinase Drug Discovery <https://www.mdpi.com/journal/ijms/special_issues/structure_guided_kinase>" A special issue of *International Journal of Molecular Sciences* <https://www.mdpi.com/journal/ijms> (IF 4.183) (ISSN 1422-0067). Email disclaimer <https://www.york.ac.uk/about/legal-statements/email-disclaimer/> -- ICREA Res. Prof. Isabel Usón Crystallographic Methods Department of Structural Biology (“Maria de Maeztu” Unit of Excellence), Molecular Biology Institute of Barcelona, Spanish Research
[ccp4bb] Beam Time for Macromolecular Crystallography at CHESS: Rapid Access Available for Fall 2019
Dear CCP4bb Users, The new and fully-upgraded macromolecular crystallography beamline at CHESS, FlexX, is now accepting Rapid Access proposals for the Fall 2019 run. Rapid Access ensures fast proposal review turnaround (two weeks or less) for access to slots still available for this run. Please include the words "RAPID ACCESS" in the proposal title when submitting for rapid turnaround. SPRING 2020 RUN: The regular proposal deadline for the Spring 2020 run is Oct. 28, 2019. The FlexX station (beamline ID7B2) is the all-new macromolecular crystallography station at CHESS. The recently completed CHESS upgrade has considerably improved our capabilities in order to meet the the stringent demands of every user. Current capabilities include: * undulator source with multilayer monochromator for high flux. 7-14 keV energy range. Standard beam sizes available: 100 x 100 um (H x V FWHM) and 10 x 10 um microbeam. * single-axis goniostat, PILATUS3 6M detector, BAM2 automounter accepting Unipucks * remote data collection with on-site CHESS staff scientist support * we welcome "non-standard" experiments! The staff at CHESS is more than happy to work with users who want to perform experiments beyond standard rotation cryocrystallography. Interested in trying serial crystallography for room-temperature data collection, or microcrystals? High-pressure cryocooling for reduced mosaicity? High-pressure crystallography with a diamond anvil cell? We can accommodate your needs and more! Interested? Learn how to submit a proposal here: https://www.chess.cornell.edu/users/new-user-guide Feel free to contact me with any questions! Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] beryllium chloride
There are plenty of heavy metals that have little to no physiological significance, because biomes evolved in their absence. But beryllium is interesting because it’s so light and nonabundant in comparison to related elements like Li or Mg. So since mammals never evolved with free Be2+ around, it can run amok, interacting with DNA and inhibiting enzymes. That said, I am sure there is a cave somewhere on earth, full of emeralds and other beryl minerals, where microbes evolved to handily deal with the beryllium monster. We just haven’t found it yet. As Ian Malcolm said, “Life, uh, finds a way.” I also just read that beryllium used to be called glucinium after the Greek for “sweet,” because many beryllium salts taste sweet. Yikes. Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 2, 2019, at 11:32 AM, Keller, Jacob mailto:kell...@janelia.hhmi.org>> wrote: I remember from biochemistry class that it’s the one element that has no known physiological role—is that still true? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Aaron Finke Sent: Tuesday, April 2, 2019 11:21 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] beryllium chloride The lung disease is called berylliosis and is an allergic-type response that leads to fibrosis in the lungs. A significant percentage of the population has allergic reactions to beryllium, but there is no very accurate method for prescreening this; I read somewhere even lung biopsies are only about 80% accurate for beryllium sensitivity. Beryllium metal readily oxidizes in air and BeO is the typical inhlation vector. Mind you, this is on top of the carginogenic properties of beryllium and its compounds. It’s just nasty stuff. Shame it’s so useful... Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 2, 2019, at 10:21 AM, Zhijie Li mailto:zhijie...@utoronto.ca>> wrote: Sometime ago when I was watching a Youtube video on magnetron I learnt that at least at at certain point of time the antenna port of the magnetron was sealed using beryllium oxide ceramic(probably for its high thermal conductivity). The video maker warned that this ceramic was extremely dangerous. Further wikipedia and internet reading confirmed that fine beryllium oxide powder does cause something called beryllium disease and cancer (the latter in a way similar to that of asbestos? I guessed). However the sintered ceramic form is probably as safe as emerald unless you have to grind it and breath the dust every day. (I think most jewellers would always use some grinding liquid when honing their stones.) The wikipedia page on beryllium oxide has some really interesting facts. Also if one is desperate for some beryllium salt it hints dissolving a magnetron antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4. My 2 cents. Zhijie On Apr 2, 2019, at 8:39 AM, Ian Tickle mailto:ianj...@gmail.com>> wrote: Yes both soluble beryllium salts and powdered beryllium metal even applied to the skin are known to cause sensitization and is a route into the bloodstream where it is highly carcinogenic (I am not speaking from experience!). Yet strangely the one source of beryllium that many people (at least the more well-off among us) commonly come into contact with, namely the gemstone emerald Be3Al2(SiO3)6 obviously has no known toxic effects whatosever! Apparently even gemstone grinders show no ill effects! I guess it's the free Be2+ ion that's so toxic. Cheers -- Ian On Tue, 2 Apr 2019 at 13:07, Aaron Finke mailto:af...@cornell.edu>> wrote: 1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 2. Bob, I studied that page, and couldn’t get past BeCl2 is known to have a “sweetish taste.” I’m very glad chemists no longer characterize chemicals by their taste anymore... -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 1, 2019, at 22:37, Sweet, Robert
Re: [ccp4bb] beryllium chloride
The lung disease is called berylliosis and is an allergic-type response that leads to fibrosis in the lungs. A significant percentage of the population has allergic reactions to beryllium, but there is no very accurate method for prescreening this; I read somewhere even lung biopsies are only about 80% accurate for beryllium sensitivity. Beryllium metal readily oxidizes in air and BeO is the typical inhlation vector. Mind you, this is on top of the carginogenic properties of beryllium and its compounds. It’s just nasty stuff. Shame it’s so useful... Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 2, 2019, at 10:21 AM, Zhijie Li mailto:zhijie...@utoronto.ca>> wrote: Sometime ago when I was watching a Youtube video on magnetron I learnt that at least at at certain point of time the antenna port of the magnetron was sealed using beryllium oxide ceramic(probably for its high thermal conductivity). The video maker warned that this ceramic was extremely dangerous. Further wikipedia and internet reading confirmed that fine beryllium oxide powder does cause something called beryllium disease and cancer (the latter in a way similar to that of asbestos? I guessed). However the sintered ceramic form is probably as safe as emerald unless you have to grind it and breath the dust every day. (I think most jewellers would always use some grinding liquid when honing their stones.) The wikipedia page on beryllium oxide has some really interesting facts. Also if one is desperate for some beryllium salt it hints dissolving a magnetron antenna sealing ring in hot concentrated solution of H2SO4 and (NH4)2SO4. My 2 cents. Zhijie On Apr 2, 2019, at 8:39 AM, Ian Tickle mailto:ianj...@gmail.com>> wrote: Yes both soluble beryllium salts and powdered beryllium metal even applied to the skin are known to cause sensitization and is a route into the bloodstream where it is highly carcinogenic (I am not speaking from experience!). Yet strangely the one source of beryllium that many people (at least the more well-off among us) commonly come into contact with, namely the gemstone emerald Be3Al2(SiO3)6 obviously has no known toxic effects whatosever! Apparently even gemstone grinders show no ill effects! I guess it's the free Be2+ ion that's so toxic. Cheers -- Ian On Tue, 2 Apr 2019 at 13:07, Aaron Finke mailto:af...@cornell.edu>> wrote: 1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 2. Bob, I studied that page, and couldn’t get past BeCl2 is known to have a “sweetish taste.” I’m very glad chemists no longer characterize chemicals by their taste anymore... ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 1, 2019, at 22:37, Sweet, Robert <27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk<mailto:27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk>> wrote: With all respect, this conversation make my skin crawl a little. I've been taught that beryllium salts are EXTREMELY toxic. Please study this: https://pubchem.ncbi.nlm.nih.gov/compound/beryllium_chloride Hopefully, Bob Robert M. Sweet E-Dress: sw...@bnl.gov<mailto:sw...@bnl.gov> Deputy Director, LSBR: The Life Science and Biomedical Technology Research Center at NSLS-II Photon Sciences and Biology Dept Brookhaven Nat'l Lab. Upton, NY 11973 U.S.A. Phones:631 344 3401 (Office) 631 338 7302 (Mobile) From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu>> Sent: Monday, April 1, 2019 7:03 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] beryllium chloride No, that should read Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Apr 1, 2019, at 5:54 PM, Keller, Jacob mailto:kell...@janelia.hhmi.org>> wrote: Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion with such a charge, well except things like DNA and proteins, but not single atoms. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The c
Re: [ccp4bb] beryllium chloride
1. Yes, I meant the tetrahydrate, [Be(H2O)4]2+ 2Cl- 2. Bob, I studied that page, and couldn’t get past BeCl2 is known to have a “sweetish taste.” I’m very glad chemists no longer characterize chemicals by their taste anymore... -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 1, 2019, at 22:37, Sweet, Robert <27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk<mailto:27e0eb9d20ec-dmarc-requ...@jiscmail.ac.uk>> wrote: With all respect, this conversation make my skin crawl a little. I've been taught that beryllium salts are EXTREMELY toxic. Please study this: https://pubchem.ncbi.nlm.nih.gov/compound/beryllium_chloride Hopefully, Bob Robert M. Sweet E-Dress: sw...@bnl.gov<mailto:sw...@bnl.gov> Deputy Director, LSBR: The Life Science and Biomedical Technology Research Center at NSLS-II Photon Sciences and Biology Dept Brookhaven Nat'l Lab. Upton, NY 11973 U.S.A. Phones:631 344 3401 (Office) 631 338 7302 (Mobile) From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Diana Tomchick mailto:diana.tomch...@utsouthwestern.edu>> Sent: Monday, April 1, 2019 7:03 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] beryllium chloride No, that should read [cid:2D6B8E73-AD29-4B8C-972A-06201D871588] Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214) 645-6353 (fax) On Apr 1, 2019, at 5:54 PM, Keller, Jacob mailto:kell...@janelia.hhmi.org>> wrote: Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion with such a charge, well except things like DNA and proteins, but not single atoms. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email is confidential and intended for the recipient specified in message only. It is strictly forbidden to share any part of this message with any third party, without a written consent of the sender. If you received this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Aaron Finke Sent: Monday, April 1, 2019 6:45 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] beryllium chloride American Elements sells BeCl2 but you’d have to check with them on what scale they sell it at. They tend to do custom manufacturing. https://www.americanelements.com/beryllium-chloride-7787-47-5 BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-. Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 1, 2019, at 17:07, Alexandra Deaconescu mailto:alexandra_deacone...@brown.edu>> wrote: Hello, Is anyone aware of a company that sells Beryllium chloride in the US? Sigma does not carry it any longer, and a quick Google search failed to reveal alternatives. Thank you very much, Alexandra -- Alexandra Deaconescu, B.E., Ph.D. Assistant Professor Brown University Office: (401) 863-3215 Wet Lab: (401) 863-6729 Computational Lab: (401) 863-7031 For Mail: Laboratories of Molecular Medicine 70 Ship St. GE-4 Providence, RI 02903 For Courier: Laboratories of Molecular Medicine Brown University 70 Ship St., Chestnut St. Loading Dock Providence, RI 02903 Website: www.deaconesculab.com<http://www.deaconesculab.com/> Admin Ms. Christina Fournier Email: christina_fournier[at]brown.edu<http://brown.edu/> Mailing Address: Box G-E, Brown University, Providence, RI 02912-G Telephone: 401-863-2782 Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message. To unsubscribe f
Re: [ccp4bb] beryllium chloride
American Elements sells BeCl2 but you’d have to check with them on what scale they sell it at. They tend to do custom manufacturing. https://www.americanelements.com/beryllium-chloride-7787-47-5 BeCl2 dissociates in aqueous solution to form Be(H2O)4+ 2Cl-. Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Apr 1, 2019, at 17:07, Alexandra Deaconescu mailto:alexandra_deacone...@brown.edu>> wrote: Hello, Is anyone aware of a company that sells Beryllium chloride in the US? Sigma does not carry it any longer, and a quick Google search failed to reveal alternatives. Thank you very much, Alexandra -- Alexandra Deaconescu, B.E., Ph.D. Assistant Professor Brown University Office: (401) 863-3215 Wet Lab: (401) 863-6729 Computational Lab: (401) 863-7031 For Mail: Laboratories of Molecular Medicine 70 Ship St. GE-4 Providence, RI 02903 For Courier: Laboratories of Molecular Medicine Brown University 70 Ship St., Chestnut St. Loading Dock Providence, RI 02903 Website: www.deaconesculab.com<http://www.deaconesculab.com> Admin Ms. Christina Fournier Email: christina_fournier[at]brown.edu<http://brown.edu> Mailing Address: Box G-E, Brown University, Providence, RI 02912-G Telephone: 401-863-2782 Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Backup of whole synchrotrons
Not to toot our own horn too much, but CHESS has been ahead of the curve on this for at least 30 years. As an academic facility, we simply take our limitless supply of graduate students, wipe their memory, upload what we need, and lock them in dimly-lit facilities. No freezing in liquid nitrogen necessary, and all they require for subsistence are cheap coffee and free pizza. To date, nobody has noticed. -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Mar 31, 2019, at 11:59 PM, Petr Kolenko mailto:petr.kole...@fjfi.cvut.cz>> wrote: Dear colleagues, We all are very happy about the storage of raw crystallographic datasets. But, is it really enough? No! Can we do better? Yes, of course! The problem is that the crystal after the measurement is usually burned. It does not make sense to store them any more. But, in order to maximize reproducibility and increase the reliability of all our results, the committee of the Czech and Slovak Crystallographic Association has decided to force our researchers to back up the whole experimental station (including synchrotrons and their storage rings) after each crystal, each use. Storage of synchrotrons under liquid nitrogen is welcomed, but not necessary, yet. For the next decade, in-house storage of complete XFELs is expected (EU project Horizon 2030, proposal EC.2030.14.1.CZ.004). Best regards, Petr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Open Access Repositories for Big Data?
This is what Zenodo emailed me: "By default, we provide a one-time quota increase up to 100GB for a dataset that will be cited from a peer-reviewed article. Zenodo is a free-to-use service, an in order to keep it this way, we have to restrict the incoming data volume rate as very large datasets contribute significantly to the overall data volume in Zenodo. Unfortunately, at this point, we also cannot receive payment for quota increases, though we do hope that this will be possible in the future, at which point we will announce this possibility.” I suppose I could split the dataset over multiple DOIs but it feels like “cheating the system” a bit. The CXIDB sounds promising, though! Thanks, Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Jan 18, 2019, at 11:16 AM, Herbert J. Bernstein mailto:yaya...@gmail.com>> wrote: The zenodo policies seem to the most workable as a start. I would suggest contacting them for the cases that go over 50GB, but at worst splitting into 50GB chunks. -- Herbert On Fri, Jan 18, 2019 at 10:49 AM Andreas Förster mailto:andreas.foers...@dectris.com>> wrote: Hi Aaron, can you slice your data and then link to the bits? We're currently trying to find out what "unlimited Google Drive storage" means by uploading pi in chunks of 70 GB or so. All best. Andreas On Fri, Jan 18, 2019 at 4:31 PM Aaron Finke mailto:af...@cornell.edu>> wrote: Dear CCP4ites, Is anyone aware of online repositories that will store huge sets of raw data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to respond to my emails. I could host them myself, but the involuntary dry heaving response I got when I brought up the idea to our IT department implied they were less enthused with the idea than I was. So a cloud service would be far more preferable as a long term solution. Thanks, Aaron ------ Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- <https://www.dectris.com/> Andreas Förster, Ph.D. Application Scientist Crystallography, Scientific Sales Phone: +41 56 500 21 00 | Direct: +41 56 500 21 76 | Email: andreas.foers...@dectris.com<mailto:andreas.foers...@dectris.com> DECTRIS Ltd. | Taefernweg 1 | 5405 Baden-Daettwil | Switzerland | www.dectris.com<https://www.dectris.com/> [https://www.dectris.com/files/content/images/signatur/logo_signatur.png] <https://www.facebook.com/pages/Dectris-Ltd/623855944369304> <https://www.linkedin.com/company/5067919><https://www.linkedin.com/company/5067919><https://www.linkedin.com/company/5067919><https://www.linkedin.com/company/5067919>[LinkedIn]<https://www.linkedin.com/company/5067919> <https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://www.facebook.com/pages/Dectris-Ltd/623855944369304>[facebook]<https://www.facebook.com/pages/Dectris-Ltd/623855944369304><https://twitter.com/DECTRIS_News><https://twitter.com/DECTRIS_News>[https://www.dectris.com/files/content/images/signatur/twitter_20px.png]<https://twitter.com/DECTRIS_News> Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or privileged information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibited. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Open Access Repositories for Big Data?
Dear CCP4ites, Is anyone aware of online repositories that will store huge sets of raw data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s limit is typically 50 GB and their absolute limit is 100 GB. SBGrid has yet to respond to my emails. I could host them myself, but the involuntary dry heaving response I got when I brought up the idea to our IT department implied they were less enthused with the idea than I was. So a cloud service would be far more preferable as a long term solution. Thanks, Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Structure solution - hexapeptide
Hi Kristof, Direct methods/charge flipping won’t work if your data quality is poor below ~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small molecule crystals have more stringent standards for data quality. If your Rmerge is 50% or more, it’s probably just noise and not useful for direct methods. If SHELXT doesn’t work on the full data set, try cutting the data down to 0.9 Å or even 1 Å. I have had limited success doing that on some particularly bad data sets. Alternatively, run SHELXD at full resolution indefinitely (NTRY 0) until it finds a solution. It could take days, but you may get something. As a last resort, if you think this hexapeptide may have any secondary structure, you may want to try ab initio MR with ARCIMBOLDO. Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke mailto:kristofrg.vanhe...@gmail.com>> wrote: Dear all, I’m trying to solve a structure of a (modified) hexapeptide: - inhouse (very decent) data up to 0.8 Angstrom - average redundancy = 10 - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there should be 3 Nmol/asym - ‘large’ unit cell of about a=54, b=54, c=12 - SG = P3(1)12 or P3(2)12 As there’s (presumably) only C, H, N and O in the structure, I’m not able to solve this via Direct Methods, Charge Flipping etc,. Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any homologous models Has anyone encountered a similar problem please, and could provide any possible solutions? (building in heavy atoms isn’t my first option at the moment,. ) Thank you very much Regards Kristof To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] processing hd5 files from Dectris detector
Sometimes neggia has hiccups with uncompressed h5 images, in which case I recommend using eiger2cbf via H5ToXDS (instructions here: https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Eiger#A_script_for_faster_XDS_processing_of_CBF-converted_Eiger_data) I have found that in most cases, using the above approach has comparable performance to neggia and does not have the compression compatibility issue. Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu> On May 31, 2018, at 3:20 PM, SAVKO Martin mailto:martin.sa...@synchrotron-soleil.fr>> wrote: Dear Laurent, you can enable xdsme to process Eiger data in hdf5 format by giving it the path to neggia plugin. For example xdsme -i "LIB= /path/to/dectris_neggia.so" collect_master.h5 This will work on both Linux and OSX/macOS provided the plugin has been compiled for the given platform. You may get the dectris neggia plugin compiled for Linux and OSX on the links below http://bit.ly/neggia_plugin_linux http://bit.ly/neggia_plugin_osx Source code is available at https://github.com/dectris/neggia.git Kind regards, Martin -- Martin Savko Synchrotron SOLEIL PROXIMA 2A L'Orme des Merisiers Saint Aubin - BP 48 91192 Gif sur Yvette Cedex France Office: +33 1 69 35 81 76 Beamline: +33 1 69 35 81 80 martin.sa...@synchrotron-soleil.fr De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de maveyrau [laurent.maveyr...@ipbs.fr] Envoyé : jeudi 31 mai 2018 14:58 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] processing hd5 files from Dectris detector Hi CCP4ers we recently collected many datasets on dectris detectors producing hd5 files. I would like to use some auto processing tools to process them (xdsapp, xdsme…). As far as I can say, xdsapp or xdsme cannot process hd5 natively. I tried to convert them to cbf format (eiger2cbf, hdf2mini-cbf,...), but then it seams that the header of the caf files are lacking some required informations… Any idea how to convert hd5 files to complete caf files ? Are there any plans for xdsapp to be able to work on hd5 files ? thanks for your help Laurent -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr P I C T --- Plateforme Intégrée de Criblage de Toulouse Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 Département BiologieStructurale et Biophysique http://cribligand.ipbs.fr http://www.ipbs.fr 205 route de Narbonne 31077 TOULOUSE Cedex FRANCE Tél: +33 (0)561 175 435 Mob.: +33 (0)646 042 111 -- To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Visualize symmetry operations
Dear CCP4-keteers, Is there a program that can visualize symmetry operation positions (e.g. twofold screws, fourfolds) in protein structures, like CCDC Mercury does for small molecules? Thanks in advance, Aaron -- Aaron Finke Staff Scientist, MacCHESS Cornell University e-mail: af...@cornell.edu<mailto:af...@cornell.edu>
