Hello,
Manual fitting in ChimeraX followed by its fitmap command is indeed quick and easy, and many people's go-to. If you want to skip the manual step, read the documentation for fitmap (the command "help fitmap" will open it), there are options for global search that can do large steps so you don't have to do them by manually moving the model. It often takes some trial and error to find good numbers for these options, but can be fully done from the keyboard (on a laptop without an external mouse, I find the "right click to move model" can be difficult to use sometimes). If you want more automation or need to run on a cluster (no graphics), these two tools in Phenix will do that: - phenix.voyager.em_placement https://phenix-online.org/documentation/reference/em_placement.html - phenix.voyager.emplace_local https://phenix-online.org/documentation/reference/emplace_local.html They are from the same group that makes Phaser. Finally, you can use emplace_local interactively from within ChimeraX, using the Phenix integration extension of ChimeraX. This is explained in these two short videos: - setup: https://www.youtube.com/watch?v=DlVgrQTZ5t8 - using emplace_local: https://www.youtube.com/watch?v=nRiumhKA6BM This last option is helpful when you have a map that is not good enough to obtain a good fit with the fitmap command. I hope this helps, Guillaume ________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Filip Van Petegem <[email protected]> Sent: Wednesday, November 27, 2024 2:19:41 AM To: [email protected] Subject: Re: [ccp4bb] cryoEM molecular replacement ChimeraX for a quick visual fit: https://www.cgl.ucsf.edu/chimerax/ On Tue, 26 Nov 2024 at 15:50, Gloria Borgstahl <[email protected]<mailto:[email protected]>> 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 -- Filip Van Petegem, PhD Professor, Dept. of Biochemistry and Molecular Biology The University of British Columbia 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: [email protected]<mailto:[email protected]> Twitter: @FilipPetegem Bluesky: @filipvanpetegem website: https:///www.vanpetegemlab.com<http://www.vanpetegemlab.com> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ######################################################################## 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/
