Inverted fit in map ?
Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/
Hi Cedric! There is a "fitmap" command and Fit in Map tool for atoms->map and map->map fitting. If you were starting from scratch, it might make more sense to fit the two maps first, and then the atoms into the maps. However, if you are fitting atoms->atoms with matchmaker, there is another option to "bring" other models along for the ride. Our website is being difficult right now but you can use help pages from the User Guide included with your download, e.g. commands help matchmaker help fitmap I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 7, 2024, at 8:08 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/ _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Cedric, This is easy to do with the ChimeraX "view position" command. First you matchmaker to align your second atomic model to the first atomic model, then you use view position to copy the positioning of the second atomic model to the second map. Here's an example. open 8k8x open 36967 from emdb open 8k90 open 36970 from edmb matchmaker #3/C to #1/C view position #4 sameAs #3 The matchmaker command sets the position of the second atomic model (the rotation matrix and translation), and the view position command copies that same rotation and translation to the 2nd map. Documentation for view position https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html#position Tom 
On Aug 7, 2024, at 8:08 AM, GOVAERTS Cédric via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Team
I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned.
Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2)
However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ?
Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker).
Thanks !
Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 <tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
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Elaine Meng -
GOVAERTS Cédric -
Tom Goddard