Movie clipping planes in chimera x
Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command:
view p1 p2 100
it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with
view name p1 view name p2
Thanks in advance, Greg
-- Gregory Martin, PhD. Staff Scientist Lab of Andrew Ward Department of Integrative Structural & Computational Biology The Scripps Research Institute La Jolla, CA 92037
Hi Greg, I ran a few tests in the 1.5 release and a recent daily build (1.6) and wasn't able to reproduce the problem -- the clipping plane(s) always seemed to move smoothly along with the rotation/translation/zoom changes. However, my tests were relatively simple and used global clipping only. Probably there is something specific in your case that does not show up in my simple tests.
Or maybe you are using an old version that had bugs in clip plane positioning or transitions?
If updating doesn't help, would you be willing to share a session with two saved views that demonstrates the problem? If so, could use menu: Help... Report a Bug and attach it along with a brief description and include your email address on the report to get feedback. Or, if you want to limit sharing to the few people on our dev team only, you could email it to me.
But if not, I understand, we will try to come up with a test that demonstrates the pathology. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2023, at 2:05 PM, Greg Martin via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command:
view p1 p2 100
it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with
view name p1 view name p2
Thanks in advance, Greg
Hi Greg,
If you save position p1 with no clipping and position p2 with clipping, then there will be no smooth interpolation of the clip planes because the first position had no clip planes. In order to get smooth interpolating, both positions must have clip plane enabled.
Tom
On Jan 13, 2023, at 2:54 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Greg, I ran a few tests in the 1.5 release and a recent daily build (1.6) and wasn't able to reproduce the problem -- the clipping plane(s) always seemed to move smoothly along with the rotation/translation/zoom changes. However, my tests were relatively simple and used global clipping only. Probably there is something specific in your case that does not show up in my simple tests.
Or maybe you are using an old version that had bugs in clip plane positioning or transitions?
If updating doesn't help, would you be willing to share a session with two saved views that demonstrates the problem? If so, could use menu: Help... Report a Bug and attach it along with a brief description and include your email address on the report to get feedback. Or, if you want to limit sharing to the few people on our dev team only, you could email it to me.
But if not, I understand, we will try to come up with a test that demonstrates the pathology. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2023, at 2:05 PM, Greg Martin via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command:
view p1 p2 100
it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with
view name p1 view name p2
Thanks in advance, Greg
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom and Elaine, Tom you were right, I didn’t realize clipping planes in p1 were not enabled. That solved the problem! Thanks so much for your help and quick replies. -Greg
From: Tom Goddard goddard@sonic.net Date: Friday, January 13, 2023 at 3:30 PM To: Greg Martin gmartin@scripps.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Movie clipping planes in chimera x Hi Greg,
If you save position p1 with no clipping and position p2 with clipping, then there will be no smooth interpolation of the clip planes because the first position had no clip planes. In order to get smooth interpolating, both positions must have clip plane enabled.
Tom
On Jan 13, 2023, at 2:54 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Greg, I ran a few tests in the 1.5 release and a recent daily build (1.6) and wasn't able to reproduce the problem -- the clipping plane(s) always seemed to move smoothly along with the rotation/translation/zoom changes. However, my tests were relatively simple and used global clipping only. Probably there is something specific in your case that does not show up in my simple tests.
Or maybe you are using an old version that had bugs in clip plane positioning or transitions?
If updating doesn't help, would you be willing to share a session with two saved views that demonstrates the problem? If so, could use menu: Help... Report a Bug and attach it along with a brief description and include your email address on the report to get feedback. Or, if you want to limit sharing to the few people on our dev team only, you could email it to me.
But if not, I understand, we will try to come up with a test that demonstrates the pathology. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 13, 2023, at 2:05 PM, Greg Martin via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi, I’m trying to make a movie where I highlight different parts of a large complex. For one scene, I’m trying to interpolate between a zoomed out view of the whole complex (view p1), and then a zoomed in view of an interface (view p2), which shows a series of interactions. What I want is a smooth transition of both the view and clipping plane from p1 to p2. However, when I give the command:
view p1 p2 100
it interpolates the two positions/zooms fine, in 100 frames, but then after the movement adjusts the clipping plane all at once. Is there a way to have the plane adjusted smoothly during transition between p1 and p2? I’ve also tried fly, but this disregards clipping planes altogether. Views are saved with
view name p1 view name p2
Thanks in advance, Greg
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Elaine Meng -
Greg Martin -
Tom Goddard