ISOLDE messes with view?
Hello, I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. Cheers, Alexis
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit. On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
The following alias should let you set everything back to factory default after you’ve used ISOLDE: alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hi Tristan, Alexis, Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should. Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com <mailto:tcroll@altoslabs.com>> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, Tristan, Thanks - that sounds like it could indeed be the root cause. Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands. Cheers, Alexis On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Alexis, The definition of zoom is not the same for perspective projection and orthographic projection, so it doesn't make sense to restore the perspective zoom in orthographic mode. ChimeraX could guess what depth you want the scaling to match. That will lead to confusion since the appearance will not be the same as when the view was named unless the camera mode is switched. Tom
On Dec 19, 2023, at 2:16 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom, Tristan,
Thanks - that sounds like it could indeed be the root cause.
Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands.
Cheers, Alexis
On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com <mailto:tcroll@altoslabs.com>> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
I see... in that case I don't know what I'd recommend. Could fly progressively switch the camera mode from perspective to ortho, say? Either way I'd definitely trust your intuition on this and not mine!! On Tue, Dec 19, 2023 at 2:32 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
The definition of zoom is not the same for perspective projection and orthographic projection, so it doesn't make sense to restore the perspective zoom in orthographic mode. ChimeraX could guess what depth you want the scaling to match. That will lead to confusion since the appearance will not be the same as when the view was named unless the camera mode is switched.
Tom
On Dec 19, 2023, at 2:16 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom, Tristan,
Thanks - that sounds like it could indeed be the root cause.
Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands.
Cheers, Alexis
On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, In my hands (1.7rc), when in ortho mode, the view command correctly recalls the zoom of views that were named while in ortho mode, but the fly command does not. When in perspective, both view and fly behave as expected. This is what I'm doing: - start ChimeraX - define views in perspective - check that "view" recalls the views correctly - works for me - check that "fly" recalls and interpolates zoom levels correctly - works for me - "camera ortho" - define new views, with new names - confirm that "view" recalls the views correctly, including zoom level - works for me - test "fly" - does it recall and interpolate zoom levels correctly? not for me Can you reproduce this? Cheers, Alexis On Tue, Dec 19, 2023 at 2:39 PM Alexis Rohou <a.rohou@gmail.com> wrote:
I see... in that case I don't know what I'd recommend. Could fly progressively switch the camera mode from perspective to ortho, say? Either way I'd definitely trust your intuition on this and not mine!!
On Tue, Dec 19, 2023 at 2:32 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
The definition of zoom is not the same for perspective projection and orthographic projection, so it doesn't make sense to restore the perspective zoom in orthographic mode. ChimeraX could guess what depth you want the scaling to match. That will lead to confusion since the appearance will not be the same as when the view was named unless the camera mode is switched.
Tom
On Dec 19, 2023, at 2:16 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom, Tristan,
Thanks - that sounds like it could indeed be the root cause.
Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands.
Cheers, Alexis
On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Alexis, You are trying to use the features in ways that no one uses them. The view and fly command are for animations and doing that in orthographic projection will be hard for most viewers to stomach since it is not how human vision works. Of course there are rare uses, and Tristan has decided orthographic is useful in ISOLDE. We should add a bit more documentation. The view command does not switch camera modes, so if you create named views in one camera mode and then try to switch to them while in a different camera mode it doesn't work as you have seen with zoom not working. The fly command handles perspective camera parameters and does not do anything with orthographic zoom level. It is reasonable to ask why not. The answer is we don't have time to implement features that are useful for very few users. Some general advice, the more you move away from the defaults in ChimeraX (e.g. perspective camera) the more you will run into undocumented weird behaviors and the more time you will spend wondering why things don't work. We don't have the resources to implement rarely used cases like flying in orthographic projection -- it is not that it is hard, it is just we could not possibly get funding if we did work of value to so few researchers. We try to document these limitations. I've tried to persuade Tristan to make ISOLDE play well will the ChimeraX defaults, but he sometimes decides something like orthographic projection is too useful for his case even though that leads you down a trail of things that don't work. Tom
On Dec 19, 2023, at 4:28 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom,
In my hands (1.7rc), when in ortho mode, the view command correctly recalls the zoom of views that were named while in ortho mode, but the fly command does not. When in perspective, both view and fly behave as expected.
This is what I'm doing: - start ChimeraX - define views in perspective - check that "view" recalls the views correctly - works for me - check that "fly" recalls and interpolates zoom levels correctly - works for me - "camera ortho" - define new views, with new names - confirm that "view" recalls the views correctly, including zoom level - works for me - test "fly" - does it recall and interpolate zoom levels correctly? not for me
Can you reproduce this?
Cheers, Alexis
On Tue, Dec 19, 2023 at 2:39 PM Alexis Rohou <a.rohou@gmail.com <mailto:a.rohou@gmail.com>> wrote:
I see... in that case I don't know what I'd recommend. Could fly progressively switch the camera mode from perspective to ortho, say? Either way I'd definitely trust your intuition on this and not mine!!
On Tue, Dec 19, 2023 at 2:32 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Alexis,
The definition of zoom is not the same for perspective projection and orthographic projection, so it doesn't make sense to restore the perspective zoom in orthographic mode. ChimeraX could guess what depth you want the scaling to match. That will lead to confusion since the appearance will not be the same as when the view was named unless the camera mode is switched.
Tom
On Dec 19, 2023, at 2:16 PM, Alexis Rohou <a.rohou@gmail.com <mailto:a.rohou@gmail.com>> wrote:
Hi Tom, Tristan,
Thanks - that sounds like it could indeed be the root cause.
Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands.
Cheers, Alexis
On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com <mailto:tcroll@altoslabs.com>> wrote: > I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit. > > On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> Hello, >> >> I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. >> >> Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. >> >> I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. >> >> Cheers, >> Alexis >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hi Tom, Fair enough! I was in movie making mode, so sticking to perspective is fine. Now that I know that ortho is what was tripping me up when I happened to have had ISOLDE running before making animations, I will know to switch to perspective in future. I don’t have a specific reason to want to do this in ortho. Thanks as always for your support & patience! Cheers, Alexis On Tue, Dec 19, 2023 at 5:15 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
You are trying to use the features in ways that no one uses them. The view and fly command are for animations and doing that in orthographic projection will be hard for most viewers to stomach since it is not how human vision works. Of course there are rare uses, and Tristan has decided orthographic is useful in ISOLDE.
We should add a bit more documentation. The view command does not switch camera modes, so if you create named views in one camera mode and then try to switch to them while in a different camera mode it doesn't work as you have seen with zoom not working. The fly command handles perspective camera parameters and does not do anything with orthographic zoom level. It is reasonable to ask why not. The answer is we don't have time to implement features that are useful for very few users.
Some general advice, the more you move away from the defaults in ChimeraX (e.g. perspective camera) the more you will run into undocumented weird behaviors and the more time you will spend wondering why things don't work. We don't have the resources to implement rarely used cases like flying in orthographic projection -- it is not that it is hard, it is just we could not possibly get funding if we did work of value to so few researchers. We try to document these limitations. I've tried to persuade Tristan to make ISOLDE play well will the ChimeraX defaults, but he sometimes decides something like orthographic projection is too useful for his case even though that leads you down a trail of things that don't work.
Tom
On Dec 19, 2023, at 4:28 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom,
In my hands (1.7rc), when in ortho mode, the view command correctly recalls the zoom of views that were named while in ortho mode, but the fly command does not. When in perspective, both view and fly behave as expected.
This is what I'm doing: - start ChimeraX - define views in perspective - check that "view" recalls the views correctly - works for me - check that "fly" recalls and interpolates zoom levels correctly - works for me - "camera ortho" - define new views, with new names - confirm that "view" recalls the views correctly, including zoom level - works for me - test "fly" - does it recall and interpolate zoom levels correctly? not for me
Can you reproduce this?
Cheers, Alexis
On Tue, Dec 19, 2023 at 2:39 PM Alexis Rohou <a.rohou@gmail.com> wrote:
I see... in that case I don't know what I'd recommend. Could fly progressively switch the camera mode from perspective to ortho, say? Either way I'd definitely trust your intuition on this and not mine!!
On Tue, Dec 19, 2023 at 2:32 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Alexis,
The definition of zoom is not the same for perspective projection and orthographic projection, so it doesn't make sense to restore the perspective zoom in orthographic mode. ChimeraX could guess what depth you want the scaling to match. That will lead to confusion since the appearance will not be the same as when the view was named unless the camera mode is switched.
Tom
On Dec 19, 2023, at 2:16 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Hi Tom, Tristan,
Thanks - that sounds like it could indeed be the root cause.
Tom, I'm not sure what the correct behavior should be. One possible complication I see is with the fly command - what would the expected behavior be there? I guess I would expect the zoom to be restored by view and fly, but the camera mode to not be changed by either of these commands.
Cheers, Alexis
On Tue, Dec 19, 2023 at 1:11 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Tristan, Alexis,
Testing shows that naming a view using the default perspective camera ("view name v1") and then using "camera ortho" and then restoring the view ("view v1") does not restore the zoom. So that is probably the problem. I'm not sure if the view command should be switching the camera modes. Maybe it should.
Tom
On Dec 19, 2023, at 1:07 PM, Tristan Croll via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
The following alias should let you set everything back to factory default after you’ve used ISOLDE:
alias clipperOff camera mono;cofr front showPivot false;mousemode left select control; mousemode left none control shift; mousemode middle none control; mousemode wheel zoom; mousemode right none shift; mousemode wheel none control; mousemode wheel none alt;mousemode wheel none shift; clip off
On Tue, 19 Dec 2023 at 21:05, Tristan Croll <tcroll@altoslabs.com> wrote:
I *think* this is probably because Clipper sets the camera to orthographic on first initialisation. I can’t recall doing much more complex than that, but I can check… possibly its custom zoom mouse mode *might* be the culprit.
On Tue, 19 Dec 2023 at 20:59, Alexis Rohou via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I've just noticed that the view command doesn't behave as expected after I have started ISOLDE.
Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored.
I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE.
Cheers, Alexis _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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participants (3)
-
Alexis Rohou -
Tom Goddard -
Tristan Croll