Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry -- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3
Hi Terry, Use the volume dialog Surface and Mesh options panel (Features menu) and change mesh line thickness (default 1) in screen pixels. Also meshes tend to look much nicer with transparency, maybe 50%. Use the color button on the volume dialog under the histogram, click the opacity checkbutton, and adjust opacity (A slider). Tom
Hey Guys,
I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser?
Thanks, Terry
Hi Terry! You can make a coarser data set: "bin" the data using Volume Filter (open from Volume Viewer's Tools menu, or main Tools menu under Volume Data). There is a command "vop bin" to do the same thing. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#bin> 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 Apr 19, 2012, at 4:56 PM, Terry Lang wrote:
Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry
Oh, Elaine probably understood your question better. If you want bigger holes in your mesh then you can just increase the step size of the volume dialog to 2 to show every other data plane. That is easier than binning. Tom
Hi Terry! You can make a coarser data set: "bin" the data using Volume Filter (open from Volume Viewer's Tools menu, or main Tools menu under Volume Data). There is a command "vop bin" to do the same thing.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#bin>
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 Apr 19, 2012, at 4:56 PM, Terry Lang wrote:
Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry
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Awesome! Thanks guys! The step size thing worked great :O) Terry On 4/19/2012 5:06 PM, Tom Goddard wrote:
Oh, Elaine probably understood your question better. If you want bigger holes in your mesh then you can just increase the step size of the volume dialog to 2 to show every other data plane. That is easier than binning.
Tom
Hi Terry! You can make a coarser data set: "bin" the data using Volume Filter (open from Volume Viewer's Tools menu, or main Tools menu under Volume Data). There is a command "vop bin" to do the same thing.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/gaussian.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#bin>
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 Apr 19, 2012, at 4:56 PM, Terry Lang wrote:
Hey Guys, I am using the Volume Viewer to look at some electron density for a figure. I'd like to use the mesh option but when I generate the figure, the mesh is too fine, even at the starting default values. Is there a way to make the mesh coarser? Thanks, Terry
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Paula Therese Lang Postdoctoral Scholar Alber Lab UC Berkeley/QB3
participants (3)
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Elaine Meng -
Terry Lang -
Tom Goddard