Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation. Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
Hi Elaine, Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA. Dose chimerax has a kinda workaround like that? Yehuda Halfon -------- Original Message -------- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, November 20, 2018 07:57 PM To: Yehuda Halfon <yehuda.halfon@weizmann.ac.il> Subject: Re: [Chimera-users] Dual transparency in chimerax CC: chimera-users@cgl.ucsf.edu Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation. Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
Oh, I didn’t realize you had to use ChimeraX for your system. As far as I know, there isn’t a control for single-layer transparency in ChimeraX yet, sorry. Elaine
On Nov 20, 2018, at 10:05 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi Elaine,
Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA. Dose chimerax has a kinda workaround like that?
Yehuda Halfon
-------- Original Message -------- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, November 20, 2018 07:57 PM To: Yehuda Halfon <yehuda.halfon@weizmann.ac.il> Subject: Re: [Chimera-users] Dual transparency in chimerax CC: chimera-users@cgl.ucsf.edu
Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects>
However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation.
Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
P.S. maybe in Chimera, you could try using “molmap” to make a surface for the rRNA, as in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> That only solves part of the problem, however, as the multiple transparent layers may not be rendered correctly.
On Nov 20, 2018, at 10:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oh, I didn’t realize you had to use ChimeraX for your system. As far as I know, there isn’t a control for single-layer transparency in ChimeraX yet, sorry. Elaine
On Nov 20, 2018, at 10:05 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi Elaine,
Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA. Dose chimerax has a kinda workaround like that?
Yehuda Halfon
-------- Original Message -------- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, November 20, 2018 07:57 PM To: Yehuda Halfon <yehuda.halfon@weizmann.ac.il> Subject: Re: [Chimera-users] Dual transparency in chimerax CC: chimera-users@cgl.ucsf.edu
Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects>
However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation.
Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, I used molmap, it look 99% like surface and it's great. Thanks a lot. Yehuda ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Tuesday, November 20, 2018 9:09 PM To: Yehuda Halfon Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Dual transparency in chimerax P.S. maybe in Chimera, you could try using “molmap” to make a surface for the rRNA, as in #3 in the surface workarounds page: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html> That only solves part of the problem, however, as the multiple transparent layers may not be rendered correctly.
On Nov 20, 2018, at 10:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Oh, I didn’t realize you had to use ChimeraX for your system. As far as I know, there isn’t a control for single-layer transparency in ChimeraX yet, sorry. Elaine
On Nov 20, 2018, at 10:05 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi Elaine,
Thanks for the help, I have to use chimerax since the regular chimera can't do surface for rRNA. Dose chimerax has a kinda workaround like that?
Yehuda Halfon
-------- Original Message -------- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, November 20, 2018 07:57 PM To: Yehuda Halfon <yehuda.halfon@weizmann.ac.il> Subject: Re: [Chimera-users] Dual transparency in chimerax CC: chimera-users@cgl.ucsf.edu
Hi Yehuda, In Chimera, by default only a single transparentl layer is shown. You can turn it off with command “~set singleLayer” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html> ...or in the Effects tool (menu: Favorites… Side View, then click the Effects tab, then uncheck “single-layer” in the “transparency” section). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects>
However, even with this option turned off, multiple transparent surfaces are still often rendered incorrectly in Chimera, a known problem. You can try it and see how it looks in your situation.
Unfortunately, this multiple-transparent-surfaces problem has not been solved in ChimeraX either, as detailed in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2018-July/000274.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2018, at 8:55 AM, Yehuda Halfon <yehuda.halfon@weizmann.ac.il> wrote:
Hi all, I want to make a picture with one protein in transparency 90 and one of its subunits in transparency 40. On thier on this works fine. But when I try them together the 40 is gone inside the whole protein. Is there a way to do it in chimerax? Yehuda Halfon
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Elaine Meng -
Yehuda Halfon