Hi I thought there is was way to color density surfaces according to the assigned color of atoms close by (i.e. when there is an a atomic structure fitted into the density), but I can't remember if this was indeed possible or how to do it. Is there a way to do this ? Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>
Hi Hernando, You can do it with Color Zone (in menu under Tools...Volume Data, also in Volume Viewer "Tools" menu). This colors surfaces to match nearby selected atoms or markers: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone...> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 8, 2013, at 9:48 AM, Hernando J Sosa wrote:
Hi I thought there is was way to color density surfaces according to the assigned color of atoms close by (i.e. when there is an a atomic structure fitted into the density), but I can't remember if this was indeed possible or how to do it. Is there a way to do this ? Thanks Hernando
Thanks Elaine that works, However I had a hard time setting the transparency. I tried selecting the atoms opacity colors but I didn't manage to made the surface transparent (neither the atoms). H. -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Tuesday, January 08, 2013 1:11 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Color surfaces Hi Hernando, You can do it with Color Zone (in menu under Tools...Volume Data, also in Volume Viewer "Tools" menu). This colors surfaces to match nearby selected atoms or markers: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone...> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 8, 2013, at 9:48 AM, Hernando J Sosa wrote:
Hi I thought there is was way to color density surfaces according to the assigned color of atoms close by (i.e. when there is an a atomic structure fitted into the density), but I can't remember if this was indeed possible or how to do it. Is there a way to do this ? Thanks Hernando
Hi Hernando, I just tried the following and it worked: (1) color atoms (opaque unless you actually wanted them to be transparent) (2) select atoms, use Color Zone (3) Ctrl-click to select surface (4) use menu: Actions... Surface... transparency [...] That makes the whole surface transparent. If you want different transparency levels for the different atoms, then you have to color the atoms with transparency. For example, I could make tyrosines transparent white with command: color 1,1,1,0.5 :tyr ...and then select atoms and then use Color Zone. Each zone's color and transparency should match that of the corresponding atom. If you prefer interactive coloring over commands, you could generate the desired transparent color in the Color Editor, then select the atoms you want to have that color and apply the color with menu: Actions... Color... from editor. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 8, 2013, at 3:23 PM, Hernando J Sosa wrote:
Thanks Elaine that works, However I had a hard time setting the transparency. I tried selecting the atoms opacity colors but I didn't manage to made the surface transparent (neither the atoms).
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Elaine Meng -
Hernando J Sosa