surface cap transparent when surface dust on ?
Hi All, I have been recently trying to color a volume by a map value... So far it worked really well using the color command.... color sample #1 map #2 offset 0.1 palette " values" But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera? Also another thing, I usually do is the following: open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes... Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent? Thanks for the hard work and the nice software! Best Bertrand
Hi Bertrand, I suspect this is a bug with “surface dust” thinking that the caps are dust and thus to be hidden. We will look into it. Without that interference from "surface dust,” in my tests the caps are colored by the map value as long as the coloring command is used after the surface has been clipped to show the caps. Tested in the current daily build. For now, you may be able to work around the problem by using a different “metric” in the “surface dust” command, say “metric area”… but it depends on your specific data, so I can’t say for sure. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#dust> Thanks for reporting the problem, and for your kind words! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 6, 2019, at 10:34 AM, bertrand beckert <bertrand.beckert@gmail.com> wrote:
Hi All, I have been recently trying to color a volume by a map value... So far it worked really well using the color command....
color sample #1 map #2 offset 0.1 palette " values"
But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera?
Also another thing, I usually do is the following:
open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft
Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes...
Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent?
Thanks for the hard work and the nice software! Best Bertrand
Hi Bertrand, I'm not sure what you mean by "the surface cap is transparent". Maybe you mean there is no surface cap at all? In my tests the clip caps and coloring of caps all worked. The one tricky part is "surface dust #1" is going to hide small surface caps if you run that command after clipping because surface caps are a submodel #1.1.1 of the surface and your dust command applies to everything under model #1. You probably don't want surface dust to effect the caps so you could just run the "surface dust #1" command before you do the clipping, then it won't apply to the caps because the cap model did not exist when surface dust was run. It may be best if surface dust did not apply to caps, but that is not how it is working right now. Tom
On Nov 6, 2019, at 10:34 AM, bertrand beckert <bertrand.beckert@gmail.com> wrote:
Hi All,
I have been recently trying to color a volume by a map value... So far it worked really well using the color command....
color sample #1 map #2 offset 0.1 palette " values"
But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera?
Also another thing, I usually do is the following:
open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft
Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes...
Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent?
Thanks for the hard work and the nice software!
Best
Bertrand
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Hi Bertrand, I changed the surface dust command so it does not effect clip caps. That will be in tonight's ChimeraX builds. Tom
On Nov 6, 2019, at 12:42 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Bertrand,
I'm not sure what you mean by "the surface cap is transparent". Maybe you mean there is no surface cap at all?
In my tests the clip caps and coloring of caps all worked. The one tricky part is "surface dust #1" is going to hide small surface caps if you run that command after clipping because surface caps are a submodel #1.1.1 of the surface and your dust command applies to everything under model #1. You probably don't want surface dust to effect the caps so you could just run the "surface dust #1" command before you do the clipping, then it won't apply to the caps because the cap model did not exist when surface dust was run. It may be best if surface dust did not apply to caps, but that is not how it is working right now.
Tom
On Nov 6, 2019, at 10:34 AM, bertrand beckert <bertrand.beckert@gmail.com <mailto:bertrand.beckert@gmail.com>> wrote:
Hi All,
I have been recently trying to color a volume by a map value... So far it worked really well using the color command....
color sample #1 map #2 offset 0.1 palette " values"
But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera?
Also another thing, I usually do is the following:
open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft
Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes...
Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent?
Thanks for the hard work and the nice software!
Best
Bertrand
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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participants (3)
-
bertrand beckert -
Elaine Meng -
Tom Goddard