Hi all
Slice'N'Dice is another option for this. It will take a structure eg an AF2 prediction, remove low-confidence portions, and split the remainder using a variety of algorithms, including based on the PAE where that is available. Originally developed for MR (https://www.biorxiv.org/content/10.1101/2022.06.30.497974v1) it can also place the split regions into an EM map using Molrep or Powerfit (em_placement arriving soon). A novel classifier and clash detection are used to assess the results. SnD is interfaced from CCP4i2, CCP4 Cloud and CCPEM Doppio (Slice only atm, Dice to follow shortly). There's also a neat interface from Moorhen.org for visualising the splitting interactively. The paper has been submitted and we'll update the bioRXiv preprint soon. Best wishes Dan On 27/11/2024 18:28, Randy John Read wrote: Caution: This email originated from outside of the University. Do not click links or open attachments unless you recognise the source of this email and know the content is safe. Check sender address, hover over URLs and don't open suspicious email attachments. Thanks Martyn! I should add that support for our docking software in CCP-EM is fairly new, but it’s developing quickly. You can run emplace_local there too, though you have to provide it with the coordinates for the search center — more graphical setup akin to the ChimeraX interface should come! Randy On 27 Nov 2024, at 10:28, Martyn Winn - STFC UKRI <00007c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk><mailto:00007c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote: Hi Gloria, I agree that ChimeraX is the easiest starting point for this. After that, the CCP-EM suite has a variety of rigid and flexible fitting methods that you can try (including em_placement in the latest). Also many validation functions, which are kind of important 😊 Our annual Icknield workshop covers these techniques, look e.g. at https://www.ccpem.ac.uk/training/icknield_2023/icknield_2023.php HTH m -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> On Behalf Of Randy John Read Sent: 27 November 2024 08:40 To: ccp4bb <ccp4bb@jiscmail.ac.uk><mailto:ccp4bb@jiscmail.ac.uk> Subject: Re: [ccp4bb] cryoEM molecular replacement Hi Gloria, Guillaume already mentioned emplace_local, so I’ll just mention that if you get a recent nightly build of Phenix and the latest version of ChimeraX (plus the Phenix UI plugin from the toolshed), you can tell it your map has symmetry, place a monomer, and then it will detect the symmetry and place all the symmetry-related copies of the monomer. (That’s assuming you imposed the symmetry during the reconstruction.) It’s still under rapid development: another new feature is to be able to account for a part of the model you’ve already placed when placing a new component. To come: something much more highly automated, like Phaser, in placing multiple copies of multiple components all in one job. Best wishes, Randy On 26 Nov 2024, at 23:50, Gloria Borgstahl <gborgst...@gmail.com><mailto:gborgst...@gmail.com> wrote: Hello Friends, We are finally using cryoEM when the crystallography got too hard! We have a crystal structure for the hexamer. What is the easiest software tool to swing a monomer or hexamer into the cryoEM density? Thank you, Gloria To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk<mailto:rj...@cam.ac.uk> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.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 http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by 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&A=1 This message was issued to members of http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk<mailto:rj...@cam.ac.uk> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.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<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/ -- Prof Daniel Rigden (He/Him) Department of Biochemistry, Cell and Systems Biology Institute of Systems, Molecular and Integrative Biology Room 101, Biosciences Building University of Liverpool Crown St., Liverpool, L69 7ZB (+44) 151 795 4467 https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/daniel-rigden/ ######################################################################## 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/
