Cross section visual of map model fit
Dear community, How do we go about creating an image like this where the density around the model is quite sharp, that is, there is almost no interference from the top or the bottom density? Tried clipping volume and volume zone; both didn’t seem to give quite the same effect. Thanks, Abhi [cid:image001.png@01DBDFC6.1AD09EC0]
Hi Abhi, I believe that this is simply an isosurface that is made to be 100% transparent, with silhoutte edges turned on to give the black outlines. E.g. open 1zik set bg white hide ribbons show atoms molmap protein 4 graphics silhouettes true volume #2 level .5 color #b2b2b200 Of course you can adjust the threshold and color interactively in the Volume Viewer, e.g. drag the vertical bar on the threshold, click the color square and use the system color editor to make the color completely transparent. You can use the "seahorse" icon on the Graphics toolbar tab to turn silhouettes on and off. See the help for the options of specific commands, e.g. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> 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 Jun 17, 2025, at 5:36 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community, How do we go about creating an image like this where the density around the model is quite sharp, that is, there is almost no interference from the top or the bottom density? Tried clipping volume and volume zone; both didn’t seem to give quite the same effect. Thanks, Abhi <image001.png>_______________________________________________ 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/
If this is from a 3D map, it can also involve masking the map around the model, using a command as follows: volume zone #2 near #4 range 2 new true #2 is the map to mask #4 is the model with atoms - could be ’sel’ as well if you have the atoms of interest selected Type ‘help volume zone’ for more details on the other params Be careful with the contour level of this masked map, should not be too low to the point where noise would be shown in the original map, although it is usually obvious when this is the case, because the contour is not as smooth as in the image you show. Greg P.
On Jun 17, 2025, at 5:36 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community,
How do we go about creating an image like this where the density around the model is quite sharp, that is, there is almost no interference from the top or the bottom density? Tried clipping volume and volume zone; both didn’t seem to give quite the same effect. Thanks, Abhi
<image001.png> _______________________________________________ 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/
[like] Das, Abhinaba reacted to your message: ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, June 18, 2025 12:50:49 AM To: Das, Abhinaba <abhinaba.das@emory.edu> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: [External] Re: [chimerax-users] Cross section visual of map model fit [You don't often get email from meng@cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Abhi, I believe that this is simply an isosurface that is made to be 100% transparent, with silhoutte edges turned on to give the black outlines. E.g. open 1zik set bg white hide ribbons show atoms molmap protein 4 graphics silhouettes true volume #2 level .5 color #b2b2b200 Of course you can adjust the threshold and color interactively in the Volume Viewer, e.g. drag the vertical bar on the threshold, click the color square and use the system color editor to make the color completely transparent. You can use the "seahorse" icon on the Graphics toolbar tab to turn silhouettes on and off. See the help for the options of specific commands, e.g. <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fgraphics.html%23silhouettes&data=05%7C02%7Cabhinaba.das%40emory.edu%7C789c4f6c12734657519908ddae0236bf%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638858046755919759%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=8b%2BVNhjQtluUzWcuNqp6s4U75ugbEUyKVHOaxlkLaIE%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes>> <https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fvolume.html%23general&data=05%7C02%7Cabhinaba.das%40emory.edu%7C789c4f6c12734657519908ddae0236bf%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638858046755941059%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=l1X4N5NWSMSEvT%2BYArDPc8ow7NTvOi9qKJ5Nxfh9uJ4%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general>> 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 Jun 17, 2025, at 5:36 PM, Das, Abhinaba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear community, How do we go about creating an image like this where the density around the model is quite sharp, that is, there is almost no interference from the top or the bottom density? Tried clipping volume and volume zone; both didn’t seem to give quite the same effect. Thanks, Abhi <image001.png>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7Cabhinaba.das%40emory.edu%7C789c4f6c12734657519908ddae0236bf%7Ce004fb9cb0a4424fbcd0322606d5df38%7C0%7C0%7C638858046755957191%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=yZkYag05Cgme1vYQC5w5d4XalU%2BjjxrkaynVFivDze0%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
participants (3)
-
Das, Abhinaba -
Elaine Meng -
Greg Pintilie