[ccp4bb] Call for Abstracts: Michael G. Rossmann Memorial Symposium at the Microscopy & Microanalysis 2021
Dear Colleagues, We cordially invite you to the “Michael G. Rossmann Memorial Symposium” at the Microscopy & Microanalysis 2021 conference, to be held in Pittsburgh, PA, Aug 1-5, 2021. This symposium focuses on the application of hybrid methods in electron microscopy of viruses, enzymes and other macromolecules, areas in which Michael was a pioneer. The symposium will feature invited talks from Prof. Hao Wu (Harvard Medical School), Prof. Rui Zhao (University of Colorado School of Medicine), and Prof. Chuan (River) Xiao (University of Texas El Paso). We invite abstracts from speakers in academics and industry at all career levels who develop and apply cutting-edge structural biology approaches to the study of viruses, viral proteins, enzymes, membrane proteins, and other systems. Ten abstracts will be selected for 15-minute oral presentations whereas the remaining abstracts will have the opportunity to be selected for poster presentations. Please note that the deadline for abstract submission is February 18, 2021. You will have the opportunity to select your preference for either in-person or virtual presentation. For additional meeting information and to register and submit your abstract, visit: https://www.microscopy.org/MandM/2021/ Deadline for abstract submission: February 18, 2021 We look forward to hosting you and learning about your exciting science at the M 2021 meeting. Sincerely, Terje Dokland (University of Alabama at Birmingham, Birmingham AL) S. Saif Hasan (University of Maryland School of Medicine, Baltimore MD) 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] Rama-Z, Ramachandran plot validation in PDB-REDO
Rama-Z is implemented in CCTBX meaning it is available to CCP4 and Phenix. Also it is reported in validation and refinement in Phenix (you get the number every time you run real- or reciprocal-space refinement!). Pavel On Mon, Jan 18, 2021 at 1:58 PM Boaz Shaanan wrote: > Hi, > Will it be possible to include the rama-z analysis in Coot (perhaps as a > plugin)? > Boaz > > Boaz Shaanan, Ph.D. > Department of Life Sciences > Ben Gurion University of the Negev > Beer Sheva > Israel > > On Jan 18, 2021 22:47, Robbie Joosten wrote: > Dear all, > > During the last CCP4 meeting, Oleg presented our collaboration with the > Phenix team, about the Ramachandran plot Z-score (or Rama-Z). Since then, > some asked for a convenient way to get this score. You are now welcome to > use: https://pdb-redo.eu/tortoize > > This is a quick and easy way to check you model. Just upload your > structure model (and restraints if you have non-standard compounds) and > press "calculate". You get the Ramachandran Z-score with an error margin > and you get the side-chain equivalent (also known as the Chi-1/Chi-2 > Z-score in WHAT_CHECK) for free. > > There are two more ways to get the score, that might be relevant for > specialized use: > 1) use the webservice to get the same values and the per-residue values in > an easy-to-parse JSON file. For example through curl with the command: curl > -F data=@1cbs_final.pdb -F > dict=@/zata/ccp4-7.1/lib/data/monomers/a/ALA.cif > https://pdb-redo.eu/tortoize. Note that the "dict" value is optional. Any > other POST on https://pdb-redo.eu/tortoize would also work. > > 2) to analyse a very large group of models you are encouraged to install > tortoize locally. It's available on https://github.com/PDB-REDO/tortoize > with a BSD license. > > The scores are also of course available after each PDB-REDO run: the > Rama-Z is one of the model quality metrics. All methods take PDB and mmCIF > formatted files as longs as they are valid, i.e. fit the current format > specification (mmCIF) or contain at least a CRYST1 record (PDB). As always, > constructive feedback is appreciated. > > If you use Rama-Z, please do cite: > Sobolev et al. A Global Ramachandran Score Identifies Protein Structures > with Unlikely Stereochemistry; Structure; > https://doi.org/10.1016/j.str.2020.08.005 > > All the best on behalf of Team REDO, > Robbie > > > > 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 > 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] Vacancy for an EMDB Coordinator at EMBL-EBI
Are you an experienced electron microscopist who is passionate about cryo-EM and cryo-ET? Would you like to influence the way the world archives its EM data, including annotation, validation, dissemination, visualisation, etc.? Are you enthusiastic about engaging with the global EM community? We are looking to recruit a Coordinator to lead the EMDB resource and activities at EMBL-EBI. This is a senior position, reporting directly to Dr Ardan Patwardhan who has overall responsibility for EMBL-EBI’s EM-archiving activities. It provides a rare and exciting opportunity for a motivated scientist with experience in this rapidly expanding and developing field to have a huge impact on how the scientific community archives, validates and re-uses EM data. More information about the role, the requirements, the benefits of working at EMBL-EBI and the application procedure can be found at: https://www.embl.org/jobs/position/EBI01761/ If you know of any suitable candidates who might be interested in this position, please forward this mail to them. Thanks! --Gerard --- Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK Head of Molecular and Cellular Structure ger...@ebi.ac.uk pdbe.org emdb-empiar.org PA: Roisin Dunloppdbe_ad...@ebi.ac.uk 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] Silicone oil for "modified microbatch"
Dear Patrick, the silicone oil you're looking for is very likely octamethyltrisiloxane (trade name BRB Silicone Oil 1 cSt): https://echa.europa.eu/substance-information/-/substanceinfo/100.003.181 You can get it from Hampton Research: https://hamptonresearch.com/product-Paraffin-Silicon-Oil-352.html or from Sigma: https://www.sigmaaldrich.com/catalog/product/aldrich/235709 Happy batch crystallization! Claude Le 19/01/2021 à 11:19, Patrick Shaw Stewart a écrit : Hi All Does anyone know where you can buy Silicone Oil Dow Corning 200/1cS nowadays? This is the silicone oil that can be mixed with regular paraffin oil to speed up evaporation in microbatch-under-oil experiments, ref below. The 1cS refers to the viscosity. We used to get this from BDH, in quite large batches, but that product is no longer available. Thx Patrick ___ D'arcy A, Elmore C, Stihle M, Johnston JE. A novel approach to crystallising proteins under oil. Journal of Crystal Growth. 1996 Oct 2;168(1-4):175-80. https://www.sciencedirect.com/science/article/pii/002202489600351X -- patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Dr Claude Sauter Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Biologie des ARNt et pathogénicité tel +33 (0)388 417 102 2 allée Conrad Roentgen fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
[ccp4bb] Silicone oil for "modified microbatch"
Hi All Does anyone know where you can buy Silicone Oil Dow Corning 200/1cS nowadays? This is the silicone oil that can be mixed with regular paraffin oil to speed up evaporation in microbatch-under-oil experiments, ref below. The 1cS refers to the viscosity. We used to get this from BDH, in quite large batches, but that product is no longer available. Thx Patrick ___ D'arcy A, Elmore C, Stihle M, Johnston JE. A novel approach to crystallising proteins under oil. Journal of Crystal Growth. 1996 Oct 2;168(1-4):175-80. https://www.sciencedirect.com/science/article/pii/002202489600351X -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 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/
