Re: [ccp4bb] Real Space refinement is broken in 0.9.8.7

[Mark Saper]

I reported this problem to Paul and to the group at least 2-3 months ago. It affects protein as well as nucleus acid.  I never heard back from Paul if a fix was in progress.  Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Faculty of Medicine Hebrew University of Jerusalem  sa...@umich.edu  |  +972 52-815-0480 On Jul 17, 2023, at 6:05 PM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: There are 9 messages totaling 3086 lines in this issue. Topics of the day:  1. General interest  2. Simulation meets neutron spectroscopy meeting  3. Clustering of distinct protein conformations across the whole PDB archive  4. real space refinement broken in COOT 0.9.8.8 EL? (4)  5. Postdoctoral Fellowship in Crystallography / CryoEM at Genentech  6. PhD position structural biology of ligand-gated ion channels ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ---------------------------------------------------------------------- Date:    Mon, 17 Jul 2023 08:45:11 +0100 From:    John R Helliwell <jrhelliw...@gmail.com> Subject: General interest Dear Colleagues, I imagine that this book on the History of Scientific Journals: Publishing at The Royal Society 1665-2015, which I have reviewed in the current issue of J Appl Cryst will be of interest:- https://journals.iucr.org/j/issues/2023/04/00/xo0198/index.html My review is open access. The book itself is also open access:- https://www.jstor.org/stable/j.ctv2gz3zp1 Best wishes, John Emeritus Professor John R Helliwell DSc ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 08:28:34 +0000 From:    Sarah Fegan - STFC UKRI <sarah.fe...@stfc.ac.uk> Subject: Simulation meets neutron spectroscopy meeting Hi all, Please see the message below forwarded on behalf of the Simulation Meets Neutron Spectroscopy meeting organisers. Best wishes, Sarah We are able to announce that the deadline for the submission of contributions for Simulation Meets Neutron Spectroscopy 2023<https://www.isis.stfc.ac.uk/Pages/SiMol-2023.aspx> (30th Oct - 1st Nov) has been extended to the 31st July, and the registration<https://forms.office.com/pages/responsepage.aspx?id=HDZmP36oWEGPYZnoLbPKyPpUYA1fZSlEgWRwn7Nn-05UNjFJQTBJMk5ESEFPMUIwQTBRS042MjlKQiQlQCN0PWcu> deadline to the 18th August. The Molecular Spectroscopy Group<https://www.isis.stfc.ac.uk/Pages/Molecular-Spectroscopy.aspx> at ISIS<https://www.isis.stfc.ac.uk/Pages/home.aspx>, together with the Ada Lovelace Centre, are hosting a meeting aimed at bringing together the simulation and neutron spectroscopy communities to generate new collaborations. Talks will showcase how state of the art simulation methods complement neutron spectroscopy measurements, providing a much more complete description of the atomistic motions of many complex materials. Topics will range from catalysis, through energy materials and biological/soft matter systems. Accommodation and conference fees are paid for by ISIS for all attendees. For UK based participants reimbursement for travel will be available. We are still taking submissions for talks/posters and will provide a mini talk format for many of those who aren't selected for a full talk. Invited Speakers: Gerald Kneller, Université d'Orléans Richard Catlow, University College London Simone Meloni, University of Ferrara Maria-Paula Marques, University of Coimbra Marina Ganeva, Julich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ) Ivana Radosavljevic, Durham University Kacper Druzbicki, Materials Physics Center, San Sebastian [cid:image001.png@01D9B890.8E787280] ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 10:21:10 +0100 From:    David Armstrong <dav...@ebi.ac.uk> Subject: Clustering of distinct protein conformations across the whole PDB archive Dear ccp4bb, The PDBe team is excited to unveil a new process for identifying protein conformational states across the Protein Data Bank (PDB) archive. Using deterministic clustering, we have developed a data pipeline that offers unprecedented insights into the structural variability of proteins. The pipeline considers all proteins in the PDB with 100% sequence identity and calculates a global dissimilarity score called "GLOCON". Chains with similar scores are clustered together. This process enables us to explore the range of conformation across protein structures, capturing both minor conformational differences and large domain movements. The results of the data pipeline are available through PDBe-KB aggregated views of proteins. Users can visualise the results per UniProt accessions using the "3D view of superposed structures" button to explore the structures in the Mol* viewer. In a number of case studies, this clustering process can indicate significant biological relevance. Some case studies, such as hexokinase, aldose reductase and KaiB, demonstrate the ability of the pipeline to identify distinct protein conformations and shed light on their biological significance. To find out more, view the full news item at https://www.ebi.ac.uk/pdbe/news/illuminating-protein-conformational-landscapes-pdb-archive We also encourage you to view our pre-print at https://doi.org/10.1101/2023.07.13.545008 If you have any questions or would like further details, please feel free to contact the team at pdbeh...@ebi.ac.uk. Kind regards, David -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 10:45:05 +0000 From:    "David Lawson (JIC)" <david.law...@jic.ac.uk> Subject: real space refinement broken in COOT 0.9.8.8 EL? Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (well, I mostly use tandem refinement) the atoms just shoot off in one direction to give a very scrambled structure, even if I am just doing final tweaks on a close to final structure. I don't know if it has something to do with the DNA restraints, because refining the protein in regions distant from the DNA seems fine, whereas working on protein regions close to the DNA, or on the DNA itself, generally results in a mess. However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the same input files, the problem goes away. Any help much appreciated, Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 10:57:26 +0000 From:    "Tsybovsky, Yaroslav (NIH/NCI) [C]" <yaroslav.tsybov...@nih.gov> Subject: Re: real space refinement broken in COOT 0.9.8.8 EL? Hello, I can confirm that this happens in 0.9.8.7. The problem is intermittent and I have not been able to determine what causes it so far. Some residues just fall apart into atoms as a result of real space refinement. Best, Yaroslav Yaroslav Tsybovsky, Ph.D. (contractor) Senior Scientist & Head Vaccine Research Center Electron Microscopy Unit Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. Post Office Box B Frederick, Maryland 21702 Phone: 301-846-7550 From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of David Lawson (JIC) Sent: Monday, July 17, 2023 6:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL? Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (well, I mostly use tandem refinement) the atoms just shoot off in one direction to give a very scrambled structure, even if I am just doing final tweaks on a close to final structure. I don't know if it has something to do with the DNA restraints, because refining the protein in regions distant from the DNA seems fine, whereas working on protein regions close to the DNA, or on the DNA itself, generally results in a mess. However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the same input files, the problem goes away. Any help much appreciated, Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ________________________________ To unsubscribe from the CCP4BB list, click the following link: Bad URL Removed - see why - https://ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=CCP4BB&A=1<Bad%20URL%20Removed%20-%20see%20why%20-%20https:/ees.sps.nih.gov/services/Pages/Anti-Virus.aspx?SUBED1=CCP4BB&A=1> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 11:53:05 +0100 From:    Jawahar Sudhamsu <jawah...@gene.com> Subject: Postdoctoral Fellowship in Crystallography / CryoEM at Genentech We have a exciting opportunity for a postdoctoral fellowship within my group (Jawahar Sudhamsu), in collaboration with Frederic de Sauvage, to work on structure determination and biochemical / biophysical characterization of proteins and protein complexes involved in the Wnt signaling cascade to better understand the molecular basis of normal cell and cancer cell signaling in this pathway. Come join our teams and perform impactful fundamental research in an exceptional scientific environment! For more details, relevant recent publications from the lab, and to apply, see here: https://careers.gene.com/us/en/job/GENEUS202302103789EXTERNALENUS/Postdoctoral-Fellow-Structural-Biology-Sudhamsu-de-Sauvage-Labs Sudhamsu ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 13:58:42 +0300 From:    Eugene Pichkur <eugene.pich...@gmail.com> Subject: Re: real space refinement broken in COOT 0.9.8.8 EL? Hi! Yes, it's been broken for a long time, but it will be fixed in Coot very soon [https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html]. A workaround is to downgrade to CCP4 v. 8.0.006 (Coot v. 0.9.8.5) through the CCP4 Update Manager. Best, Eugene On Mon, Jul 17, 2023 at 1:45 PM David Lawson (JIC) <david.law...@jic.ac.uk> wrote: Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (well, I mostly use tandem refinement) the atoms just shoot off in one direction to give a very scrambled structure, even if I am just doing final tweaks on a close to final structure. I don’t know if it has something to do with the DNA restraints, because refining the protein in regions distant from the DNA seems fine, whereas working on protein regions close to the DNA, or on the DNA itself, generally results in a mess. However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the same input files, the problem goes away. Any help much appreciated, Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk ------------------------------ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ Date:    Mon, 17 Jul 2023 11:46:43 +0000 From:    "David Lawson (JIC)" <david.law...@jic.ac.uk> Subject: Re: real space refinement broken in COOT 0.9.8.8 EL? Hi Eugene, Many thanks – that’s sorted it! Best wishes Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> From: Eugene Pichkur <eugene.pich...@gmail.com> Sent: Monday, July 17, 2023 11:59 AM To: David Lawson (JIC) <david.law...@jic.ac.uk> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] real space refinement broken in COOT 0.9.8.8 EL? You don't often get email from eugene.pich...@gmail.com<mailto:eugene.pich...@gmail.com>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi! Yes, it's been broken for a long time, but it will be fixed in Coot very soon [https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html]. A workaround is to downgrade to CCP4 v. 8.0.006 (Coot v. 0.9.8.5) through the CCP4 Update Manager. Best, Eugene On Mon, Jul 17, 2023 at 1:45 PM David Lawson (JIC) <david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>> wrote: Hi All, Is it just me, but is real space refinement broken in COOT 0.9.8.8 EL? I am seeing this working through CCP4i2 (CCP4-8.0.012) and CCP4 cloud (v 1.7) on an M1 iMac (running Monterey 12.6.7). I am working on a protein-DNA complex and finding that often when I do real space refinement (well, I mostly use tandem refinement) the atoms just shoot off in one direction to give a very scrambled structure, even if I am just doing final tweaks on a close to final structure. I don’t know if it has something to do with the DNA restraints, because refining the protein in regions distant from the DNA seems fine, whereas working on protein regions close to the DNA, or on the DNA itself, generally results in a mess. However, if I revert to COOT 0.9.6 EL (as distributed with CCP4-7) with the same input files, the problem goes away. Any help much appreciated, Dave ------------------------------- Prof. David M. Lawson Department of Biochemistry and Metabolism, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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://ww ------------------------------ Date:    Mon, 17 Jul 2023 11:47:58 +0000 From:    Chris Ulens <chris.ul...@kuleuven.be> Subject: Re: PhD position structural biology of ligand-gated ion channels Dear members of the community, A PhD position is available in the Laboratory of Prof. Chris Ulens, KU Leuven, Belgium (http://www.xtal.be). The research in the Laboratory of Structural Neurobiology is aimed at understanding the molecular mechanism of ligand-gated ion channels. Our methods rely on X-ray crystallography and cryo-EM in combination with electrophysiological recordings and fluorescence-based techniques. We have access to an integrated macromolecular crystallization facility with a Mosquito crystallization robot and two RockImagers. We have access to a 200 kV Glacios microscope on campus as well as 300 kV JEOL CryoARM300 at the nearby EM facility in Brussels. Current projects are situated at the crossroads of structural elucidation and drug discovery of different pentameric ligand-gated ion channels. We would like to recruit a PhD student with prior experience in purification, cryo-EM or X-ray crystallography of membrane proteins. The position is open immediately and applications will be accepted until the position is filled. Applicants are requested to submit a CV with publication list and two references. E-mail to chris.ul...@kuleuven.be Selection of recent publications: The molecular mechanism of snake short-chain α-neurotoxin binding to muscle-type nicotinic acetylcholine receptors. Nys M, Zarkadas E, Brams M, Mehregan A, Kambara K, Kool J, Casewell NR, Bertrand D, Baenziger JE, Nury H, Ulens C. Nat Commun. 2022 Aug 4;13(1):4543. The structural basis for an on-off switch controlling Gβγ-mediated inhibition of TRPM3 channels. Behrendt M, Gruss F, Enzeroth R, Dembla S, Zhao S, Crassous PA, Mohr F, Nys M, Louros N, Gallardo R, Zorzini V, Wagner D, Economou A, Rousseau F, Schymkowitz J, Philipp SE, Rohacs T, Ulens C, Oberwinkler J. Proc Natl Acad Sci U S A. 2020;117(46):29090-29100. doi: 10.1073/pnas.2001177117. Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT3 receptor via a common vestibule site. Brams M, Govaerts C, Kambara K, Price KL, Spurny R, Gharpure A, Pardon E, Evans GL, Bertrand D, Lummis SC, Hibbs RE, Steyaert J, Ulens C. Elife. 2020;9:e51511. doi: 10.7554/eLife.51511. A lipid site shapes the agonist response of a pentameric ligand-gated ion channel. Hénault CM, Govaerts C, Spurny R, Brams M, Estrada-Mondragon A, Lynch J, Bertrand D, Pardon E, Evans GL, Woods K, Elberson BW, Cuello LG, Brannigan G, Nury H, Steyaert J, Baenziger JE, Ulens C. Nat Chem Biol. 2019;15(12):1156-1164. doi: 10.1038/s41589-019-0369-4. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/ ------------------------------ End of CCP4BB Digest - 16 Jul 2023 to 17 Jul 2023 (#2023-179) ************************************************************* To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1