Good Morning, I have a cryoEM map and a pdb, after fitting them i see an extra density i can´t explain with my model (pdb), is there an easy way, in chimera (old version), to show only that extra density? Thanks M
Hi Maria, You can use the command "molmap" (Chimera or ChimeraX) to make an approximate map from your atomic structure, then "vop subtract" in Chimera or "volume subtract" in ChimeraX to subtract that map from your original map. See their respective help pages depending on which program you are using. (if you want to ask for Chimera only you should use the other email address, chimera-users@cgl.ucsf.edu -- we try not to make users confused about which program we are discussing) 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 Jul 23, 2025, at 2:27 AM, maria l via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good Morning, I have a cryoEM map and a pdb, after fitting them i see an extra density i can´t explain with my model (pdb), is there an easy way, in chimera (old version), to show only that extra density?
Thanks M _______________________________________________ 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 Maria, Subtracting the map computed from the atomic model from the cryoEM map will probably leave a lot of density where the atomic model was because the computed density from the atoms won't match the cryoEM density too well. If you want to set the density where the atomic model sits to zero you could instead use the mask command in Chimera or the ChimeraX "volume mask". Here is an example of the ChimeraX syntax volume mask #1 surface #3 invert true where #1 is the cryoEM map and #3 is the molmap computed map from the atomic model as described by Elaine. Tom
On Jul 23, 2025, at 9:12 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Maria, You can use the command "molmap" (Chimera or ChimeraX) to make an approximate map from your atomic structure, then "vop subtract" in Chimera or "volume subtract" in ChimeraX to subtract that map from your original map. See their respective help pages depending on which program you are using.
(if you want to ask for Chimera only you should use the other email address, chimera-users@cgl.ucsf.edu -- we try not to make users confused about which program we are discussing)
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 Jul 23, 2025, at 2:27 AM, maria l via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Good Morning, I have a cryoEM map and a pdb, after fitting them i see an extra density i can´t explain with my model (pdb), is there an easy way, in chimera (old version), to show only that extra density?
Thanks M _______________________________________________ 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/
_______________________________________________ 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/
participants (3)
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Elaine Meng -
maria l -
Tom Goddard