Independent movement of chains in movie
Dear ChimeraX team and list subscribers,
I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B.
If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B
However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B
I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A
I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that.
I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic?
Thank you for any pointers you might be able to share! Caroline
Dear Caroline, I'm not sure why your command
move x -1 10 atoms /A; move x 1 10 atoms /B
doesn't work... maybe there is a bug in the parsing of this syntax, or maybe the documentation needs to be revised. We will need to take a look at that.
However, you can accomplish this gradual translation of the two chains in opposite directions by combining "move" with "perframe." I tested the following in ChimeraX 1.6 just now and it works:
perframe "move x 1 atoms /A; move x -1 atoms /B" frames 10
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2023, at 4:43 AM, Caroline Stone (JIC) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX team and list subscribers,
I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B.
If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B
However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B
I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A
I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that.
I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic?
Thank you for any pointers you might be able to share! Caroline
Hi Caroline,
The fact that the "atoms" option of the move command does not work when you specify a number of frames is a bug. It will be fixed in tomorrow's daily build and ChimeraX 1.7 release candidate.
Tom
On Nov 30, 2023, at 10:42 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Caroline, I'm not sure why your command
move x -1 10 atoms /A; move x 1 10 atoms /B
doesn't work... maybe there is a bug in the parsing of this syntax, or maybe the documentation needs to be revised. We will need to take a look at that.
However, you can accomplish this gradual translation of the two chains in opposite directions by combining "move" with "perframe." I tested the following in ChimeraX 1.6 just now and it works:
perframe "move x 1 atoms /A; move x -1 atoms /B" frames 10
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2023, at 4:43 AM, Caroline Stone (JIC) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX team and list subscribers,
I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B.
If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B
However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B
I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A
I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that.
I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic?
Thank you for any pointers you might be able to share! Caroline
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/
Dear Elaine and Tom,
Thank you both for the work-around and for addressing the bug so quickly!
Best wishes, Caroline
________________________________ From: Tom Goddard goddard@sonic.net Sent: 30 November 2023 18:57 To: ChimeraX Users Help chimerax-users@cgl.ucsf.edu; Elaine Meng meng@cgl.ucsf.edu Cc: Caroline Stone (JIC) Caroline.Stone@jic.ac.uk Subject: Re: [chimerax-users] Independent movement of chains in movie
Hi Caroline,
The fact that the "atoms" option of the move command does not work when you specify a number of frames is a bug. It will be fixed in tomorrow's daily build and ChimeraX 1.7 release candidate.
Tom
On Nov 30, 2023, at 10:42 AM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Caroline, I'm not sure why your command
move x -1 10 atoms /A; move x 1 10 atoms /B
doesn't work... maybe there is a bug in the parsing of this syntax, or maybe the documentation needs to be revised. We will need to take a look at that.
However, you can accomplish this gradual translation of the two chains in opposite directions by combining "move" with "perframe." I tested the following in ChimeraX 1.6 just now and it works:
perframe "move x 1 atoms /A; move x -1 atoms /B" frames 10
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 30, 2023, at 4:43 AM, Caroline Stone (JIC) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX team and list subscribers,
I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B.
If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B
However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B
I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A
I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that.
I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic?
Thank you for any pointers you might be able to share! Caroline
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 Caroline,
I would not expect your command
cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
to rotate the two chains about the correct center. You instead would want
turn y -1 90 atoms /A center /A; turn y 1 90 atoms /B center /B
Your original command I think will turn the chain A atoms about the center of the B atoms because the 90 frames happen after all those command complete and the center of rotation is /B so both turn commands will be using the center /B. So instead you want to use the "center" option of the turn command.
Tom
On Nov 30, 2023, at 4:43 AM, Caroline Stone (JIC) via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear ChimeraX team and list subscribers,
I am making a little movie to show a complex of two proteins, but am stuck on individual movements of chain /A and /B.
If I use the move command, chain /A and /B both move independently, away from each other: move x -10 atoms /A; move x 10 atoms /B
However, if I attempt to do the same movement by going -1 or +1 over a series of 10 frames, I no longer get any movement of /A and /B. move x -1 10 atoms /A; move x 1 10 atoms /B
I can achieve movement over a number of frames, but both chains move although I tried to specify only /A. I did this based on "move axis [ distance [ frames ]]". move x -1 10 atoms /A
I feel I might be on the right track because when I use turn, I am able to trigger simultaneous independent rotation of /A and /B around their own axes (thank you for this feature by the way, last time I wondered about this it wasn't possible). cofr /A; turn y -1 90 atoms /A; cofr /B; turn y 1 90 atoms /B
My ultimate goal is to open the binding interface up a bit like opening a book. I suppose I could achieve a similar effect by setting the centre of rotation for each chain behind, rather than within - if independent movement over a series of frames isn't possible, I might experiment with that.
I updated to version 1.6 and searched the list, but I still see this behaviour with the move command. Perhaps I am missing something basic?
Thank you for any pointers you might be able to share! Caroline
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/
participants (3)
-
Caroline Stone (JIC) -
Elaine Meng -
Tom Goddard