I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan
Other graphical improvements are in "in the works", but we haven't set a timeframe yet. Improving the shadow resolution is relatively easy, so I've added a ticket with you as the reporter, so you'll be notified when the daily build has that feature in it.
- Greg
On Mon, 16 Nov 2009, Dan Gurnon wrote:
I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan
Hi Dan,
Glad you liked Chimera glossy lighting. It is computing the lighting at each pixel instead of at each surface vertex. It also improves the appearance of transparent surfaces. A patch of surface viewed nearly edge on appears more opaque then a face on patch because you are looking through a thicker section. The normal lighting does not make this correction. It makes the transparent surfaces look more 3 dimensional.
A few other rendering quality improvements are in Chimera 1.4. Silhouette edges now work with transparent surfaces. And there is a one-layer transparency option that shows only the front-most layer of a transparent surface. This allows models underneath to be seen (e.g. a molecular model) without the confusing overlaps of parts of the surface in the back showing. This is on by default for molecular surfaces (Actions / Surface / show) and is an option in volume data surfaces under the surface and mesh options panel in the volume dialog (default off).
Interactive ambient occlusion lighting is hard, though definitely useful. For special images you can sometimes fake it in Chimera as described here:
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#ambient
Different surface inside and outside colors is on our request list, item 131, since feb 2008.
http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests
Would be nice. Not too hard, but also it seems of value in limited circumstances since most clipped surfaces are "capped" i.e. the hole created by clipping is covered so the object appears solid, so the inside is not visible.
Tom
-------- Original Message -------- Subject: [Chimera-users] lighting in Chimera From: Dan Gurnon To: chimera-users Date: 11/16/09 10:26 AM
I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan
-- ____________________________
Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135
Hi Chimera Team, I am sure this is a super dumb question but I have searched the documentation quite extensively and can;t seem to find a solution. I am trying to make a movie where I move through a tomogram in planes using the command:
volume #1 planes z,200,0,1,1 wait
But the wait does not seem to work - it just skips right to the next command and gets all snarled up. I can explicitly put in the number of frames but then the timing of the movie is all messed up.
Any suggestions much appreciated. I also would rather be showing all 3 planes at the same time while I movie through the slab this but I can;t seem to find the right command to do that in a script. Thanks for any help you can provide, Best regards, Bridget
---------------------------------------------------------------------------------------------------------------------------------- Bridget Carragher, Associate Professor Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, La Jolla, CA 92037 tel: (858) 784-9070; fax: (858) 784-9090; bcarr@scripps.edu; http://ami.scripps.edu National Resource for Automated Molecular Microscopy: http://nramm.scripps.edu ----------------------------------------------------------------------------------------------------------------------------------
Hi Bridget,
Unfortunately the wait command without specifying a number of frames does not work correctly for the volume planes command. I'll record a request to fix this. So you have to specify the number of frames to wait. It should work if you specify 201 frames to wait since you are showing planes 200 to 0. To show 3 adjacent planes the last paramter should be 3. So the commands are:
volume #1 planes z,200,0,1,3 wait 201
I tried this and it worked correct in the current Chimera daily build.
Tom
Hi Chimera Team, I am sure this is a super dumb question but I have searched the documentation quite extensively and can;t seem to find a solution. I am trying to make a movie where I move through a tomogram in planes using the command:
volume #1 planes z,200,0,1,1 wait
But the wait does not seem to work - it just skips right to the next command and gets all snarled up. I can explicitly put in the number of frames but then the timing of the movie is all messed up.
Any suggestions much appreciated. I also would rather be showing all 3 planes at the same time while I movie through the slab this but I can;t seem to find the right command to do that in a script. Thanks for any help you can provide, Best regards, Bridget
Bridget Carragher, Associate Professor Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, La Jolla, CA 92037 National Resource for Automated Molecular Microscopy: http://nramm.scripps.edu
OK, thanks Tom. Any tips on how to do all three planes at once - or rather keep the others constant while eating though the side plane. I have sen movies like this but can;t seem to figure out how to do it in Chimera. Bridget
Hi Bridget,
Oh, now I understand what you meant by 3 planes. The only way to show orthogonal planes is to open additional copies of the volume and show the needed planes with those copies. A trouble you will encounter with this is that Chimera does not handle more than one transparent models correctly. So it may appear that a plane in back is actually drawn on top of a plane in front. To avoid this you can make some of the planes opaque using the Solid Rendering Options panel of the volume dialog to switch to color mode to single-color opaque. Another way to handle it is load the models in such a way that the lowest model number is the back-most plane -- that will assure it is drawn first, and higher model id numbers will get drawn in front of that. I use the opaque setting instead.
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] Chimera movie question From: Tom Goddard goddard@cgl.ucsf.edu To: Bridget Carragher bcarr@scripps.edu Date: 1/24/10 9:54 PM
Hi Bridget,
Unfortunately the wait command without specifying a number of frames does not work correctly for the volume planes command. I'll record a request to fix this. So you have to specify the number of frames to wait. It should work if you specify 201 frames to wait since you are showing planes 200 to 0. To show 3 adjacent planes the last paramter should be 3. So the commands are:
volume #1 planes z,200,0,1,3 wait 201
I tried this and it worked correct in the current Chimera daily build.
Tom
Hi Chimera Team, I am sure this is a super dumb question but I have searched the documentation quite extensively and can;t seem to find a solution. I am trying to make a movie where I move through a tomogram in planes using the command:
volume #1 planes z,200,0,1,1 wait
But the wait does not seem to work - it just skips right to the next command and gets all snarled up. I can explicitly put in the number of frames but then the timing of the movie is all messed up.
Any suggestions much appreciated. I also would rather be showing all 3 planes at the same time while I movie through the slab this but I can;t seem to find the right command to do that in a script. Thanks for any help you can provide, Best regards, Bridget
Bridget Carragher, Associate Professor Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute, MC CB129,10550 North Torrey Pines Road, La Jolla, CA 92037 National Resource for Automated Molecular Microscopy: http://nramm.scripps.edu
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Bridget,
I put an example animation on the Chimera web site in the animation gallery called "Herpes virus slices". There is also a link to a command script which makes this movie. You just use File/Open... in Chimera to run the command script.
http://www.cgl.ucsf.edu/chimera/animations/animations.html
Tom
OK, thanks Tom. Any tips on how to do all three planes at once - or rather keep the others constant while eating though the side plane. I have sen movies like this but can;t seem to figure out how to do it in Chimera. Bridget
participants (5)
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Bridget Carragher -
Dan Gurnon -
Greg Couch -
Thomas Goddard -
Tom Goddard