April 2020 - phenixbb - phenix-online.org

RapiData 2020 applications open
by Smith, Clyde 16 Nov '21

16 Nov '21

Applications are now open for the 2020 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held in sunny California at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 30 - April 4 2020. Course organizers for 2020 are Silvia Russi, Clyde Smith and Jeney Wierman. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. The application deadline is November 10 2019. Successful applicants will be notified shortly thereafter, and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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13th CCP4/APS Crystallographic School in the US
by Xu, Qingping 24 Jun '20

24 Jun '20

Dear Colleagues, We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php. Dates: June 15 through 22, 2020 Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website. Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 1th, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>. Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals). We hope to see you at the school. Charles, Garib and Qingping

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Phenix 1.18 RSR runtime
by Hannah Bridges 02 May '20

02 May '20

Dear Phenix developers, We have updated to phenix version 1.18-3845-000 and found that realspace refinement (5 cycles) with minimization global, local grid search and ADP is taking about 36 hours, compared to ~ 1hr in versions 1.17 and 1.16. The slow step is the local grid search which is taking >6 hours each cycle. We are very glad for the option to run the job detached, but I wondered if this sort of timing was expected for this version? Best wishes Hannah -- Dr Hannah Bridges Investigator Scientist MRC Mitochondrial Biology Unit The Keith Peters Building University of Cambridge Cambridge Biomedical Campus Hills Road Cambridge CB2 0XY United Kingdom Telephone : 01223 252812

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off-topic; suggestions for 96head liquid handler
by Georg Mlynek 30 Apr '20

30 Apr '20

Dear Scientific community, we have lend over Viaflow96 liquid handler (used for pipetting 35-50 uL in 96 well crystallization plates) to our Covid -19 Diagnostics Initiative. As we believe that this story will be ongoing for some longer time I am looking for a new 96 head liquid handler. We are happy with the Viaflow and have two heads 10-300 uL; 0.5-12.5 uL. However one tip box (96 tips for the 10-300 uL) is about 4 €. This compares to ~1 € for the refilling racks we use for our single channel pipettes (It is said that boxes have to be more rigid, because of pressure during tip loading). Therefore if you have a 96 head liquid handler for volumes of 20-60 uL where cheap tips can be used (automation not necessary) please write me. Many thanks in advance, best regards, Georg.

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Computational Crystallography Newsletter (CCN) release and submissions
by Nigel Moriarty 28 Apr '20

28 Apr '20

Folks Recent world events have affected many things including the timely release of the CCN. Please consider this the Shelter-In-Place edition. Many of you will be involved in SARS-CoV-2 research and the CCN for July 2020 can be a vehicle for publishing the more community interest details. The deadline for submissions is 1 JUN 2020. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Open postdoc positions in the Gonen lab
by Johan Hattne 26 Apr '20

26 Apr '20

Dear all; We would like to draw your attention to two HHMI-funded postdoc positions in the laboratory of Tamir Gonen at the University of California, Los Angeles. The first position concerns the biochemistry of membrane proteins, the second is focused on computational methods development. For further information, as well as application instructions, see the links below. Biochemistry https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… Programming https://hhmi-openhire.silkroad.com/epostings/index.cfm?fuseaction=app.jobin… // Best wishes; Johan

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Two conformation of a ligand
by Muhammad Bashir Khan 22 Apr '20

22 Apr '20

Hi All; I have a structure where I believe that the ligand is bind in two conformations. In the Ligand Fit, it places only one even I select conformer 2. My other question is, Is there a way that I can use a reference PDB bound to the ligand in the Ligand Fit to help it placing my ligand. Thanks for your help in advance Bashir -- ------------------------------------------------------ Muhammad Bashir Khan, Ph.D. Research Associate Department of Biochemistry Medical Science Bldg. Lab 3-27 University of Alberta Edmonton AB, T6G 2H7 Phone: 780-492-4577- e-mail: mbk(a)ualberta.ca <cbrooks1(a)ualberta.ca>

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Problems displaying disulphide links
by Urvashi Sharma 21 Apr '20

21 Apr '20

Dear all, I have a problems displaying disulphide links in PyMoL and CCP4mg for a 2.3 angstrom crystal structure. I have tried both PyMoL and CCP4mg, these programs are not recognizing an important inter-domain disulphide bridge which seems to have no problems in "Coot". While other intra-domain disulphide links are fine. Can anyone suggest how to manually fix it? In addition, I have performed protein-protein docking using this crystal structure and have obtained nice convincing model. However, in this pose, which is being refined and energy minimized, none of the disulphide links are intact! Upon manual examination, I have noticed that the corresponding cysteine are 3.0-4.0 angstrom away. How should I correct this? Looking forward to your suggestions... With thanks and regards, Urvashi ---------------------------------------------------- Dr Urvashi Sharma, DBT-Ramalingaswamy faculty fellow JNU, New Delhi.

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Error log
by Viswanathan Chandrasekaran 16 Apr '20

16 Apr '20

Hi all, Other than resubmitting the job, is there a way to retrieve the contents of the Phenix error dialog box that appears at the end of a failed job? It is not present in the log file. Thanks, Vish

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iNEXT-Discovery: Access to facilities for structural biology research
by a.perrakis＠nki.nl 16 Apr '20

16 Apr '20

Dear all, While being in turbulent times, iNEXT-Discovery, the EC Horizon-2020 project offering access to facilities for structural biology (EM, NMR, X-rays and macromolecular biophysics), has officially started its operations. iNEXT-Discovery encourages applications for structural biology projects for ‘translational research projects’ in the areas of biomedicine, biotechnology, biomaterials and in the food sector, in particular from non-experts and for researchers from academia and industry. We are now happy to announce to the wider research community our new website with details about the project and where applications for access to the participating facilities can be submitted: https://inext-discovery.eu<https://inext-discovery.eu/> Regardless of current corona-measures external researchers are more than welcome to apply for access and we expect reviewing of incoming proposals to proceed as normal. However, please keep in mind that most facilities are currently not operational, and it is uncertain when they will open again to deliver access and to receive visitors. We will not be able to give a detailed overview about the status of all facilities, as the situation is changing almost daily. Having accepted applications in our access pipelines will help both our scheduling and yours. Our facilities can arrange experiments for approved user projects to be executed immediately after local policies allow. Please note that applications addressing SARS-CoV-2 or Covid-19 and mentioning this in the title will be funneled towards rapid review. Operational facilities will prioritize such projects if they can be accommodated. On behalf of the iNEXT-Discovery team, Hans Wienk (Project Manager) - email h.wienk.AT.nki.nl<http://h.wienk.at.nki.nl/> for questions about access Anastassis Perrakis (Coordinator)

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