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 > <[email protected]> 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 <[email protected]> On Behalf Of Randy John Read > Sent: 27 November 2024 08:40 > To: ccp4bb <[email protected]> > 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 <[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 > > ----- > 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: > [email protected] > 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: [email protected] 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, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
