How to zoom into a spot that is not located in the center gradually and straightly?
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve
Hi Steve, Not sure if it will solve the problem, but you could try saving views (“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions. Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine! This is exactly what I want. ============= # save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step? Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Steve, Not sure if it will solve the problem, but you could try saving views (“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions. Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a
straight line. If it's not, it's really difficult to get there through a straight line.
I tried something like this in a "movie" script, but it's still not
straight.
========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view
through a straight line.
Steve
Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
--
Steve Chou
Hi Steve, You can use other commands with frame arguments (perframe, etc.) to do other things at the same time as the movement transitions. In a command file, if you put multiple commands on the same line separated by semicolons (and no “wait” command between), they start executing at the same time. http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html
See the general information about making movies http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
…and scripting with command files http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
To divide into more positioning stages, you would have to save more views at the intermediate positions. Each transition would still be pairwise between two views.
In Chimera we had “scenes” that included not only position but also display styles and colors, and transitions between scenes, but they are not currently available in ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 6:04 AM, Steve Chou stevezchou@gmail.com wrote:
Thanks Elaine! This is exactly what I want.
# save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step? Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, Not sure if it will solve the problem, but you could try saving views (“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions. Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, It looks like 'perframe' command allows me to execute multiple commands at the same time. Is it possible to run one command for 4 frames, and the other 4 commands sequentially at each frame? ============ command 1: view view_a 4 #### transit to view_a in 4 frames/steps command 2: transparency #1 50 target s #### on frame 1 command 3: color # 2 magenta target c #### on frame 2 command 4: display #1/A:10 #### on frame 3 command 5: transparency #3 20 target c #### on frame 4 ============ Steve
On Thu, Feb 21, 2019 at 11:15 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Steve, You can use other commands with frame arguments (perframe, etc.) to do other things at the same time as the movement transitions. In a command file, if you put multiple commands on the same line separated by semicolons (and no “wait” command between), they start executing at the same time. http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html
See the general information about making movies http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
…and scripting with command files < http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-f...
To divide into more positioning stages, you would have to save more views at the intermediate positions. Each transition would still be pairwise between two views.
In Chimera we had “scenes” that included not only position but also display styles and colors, and transitions between scenes, but they are not currently available in ChimeraX. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 6:04 AM, Steve Chou stevezchou@gmail.com wrote:
Thanks Elaine! This is exactly what I want.
# save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it
possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step?
Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, Not sure if it will solve the problem, but you could try saving views
(“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions.
Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through
a straight line. If it's not, it's really difficult to get there through a straight line.
I tried something like this in a "movie" script, but it's still not
straight.
========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view
through a straight line.
Steve
Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Probably. Just read the provided information about command files and making movies (links in my previous reply) including links from those pages to example movie files and tutorials, and experiment with executing your file containing some combination of action commands and “wait” commands to delay when the action commands start.
Whenever I make a script it involves a lot of trial and error, (re)executing the script and adjusting it. Just try it rather than asking here about each detail in your movie.
I suspect you will really be using much larger frame numbers, as 4 frames will happen in the blink of an eye. The “making movies” page has a discussion of frame rate at the bottom. Elaine
On Feb 21, 2019, at 9:38 AM, Steve Chou stevezchou@gmail.com wrote:
Hi Elaine, It looks like 'perframe' command allows me to execute multiple commands at the same time. Is it possible to run one command for 4 frames, and the other 4 commands sequentially at each frame? ============ command 1: view view_a 4 #### transit to view_a in 4 frames/steps command 2: transparency #1 50 target s #### on frame 1 command 3: color # 2 magenta target c #### on frame 2 command 4: display #1/A:10 #### on frame 3 command 5: transparency #3 20 target c #### on frame 4 ============ Steve
On Thu, Feb 21, 2019 at 11:15 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, You can use other commands with frame arguments (perframe, etc.) to do other things at the same time as the movement transitions. In a command file, if you put multiple commands on the same line separated by semicolons (and no “wait” command between), they start executing at the same time. http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html
See the general information about making movies http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
…and scripting with command files http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
To divide into more positioning stages, you would have to save more views at the intermediate positions. Each transition would still be pairwise between two views.
In Chimera we had “scenes” that included not only position but also display styles and colors, and transitions between scenes, but they are not currently available in ChimeraX. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 6:04 AM, Steve Chou stevezchou@gmail.com wrote:
Thanks Elaine! This is exactly what I want.
# save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step? Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, Not sure if it will solve the problem, but you could try saving views (“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions. Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
It seems that "view" info is not saved in .cxs file. After I save the session, and open it the next time, 'view list' says 'No named views'. Steve
On Thu, Feb 21, 2019 at 2:18 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Probably. Just read the provided information about command files and making movies (links in my previous reply) including links from those pages to example movie files and tutorials, and experiment with executing your file containing some combination of action commands and “wait” commands to delay when the action commands start.
Whenever I make a script it involves a lot of trial and error, (re)executing the script and adjusting it. Just try it rather than asking here about each detail in your movie.
I suspect you will really be using much larger frame numbers, as 4 frames will happen in the blink of an eye. The “making movies” page has a discussion of frame rate at the bottom. Elaine
On Feb 21, 2019, at 9:38 AM, Steve Chou stevezchou@gmail.com wrote:
Hi Elaine, It looks like 'perframe' command allows me to execute multiple commands
at the same time. Is it possible to run one command for 4 frames, and the other 4 commands sequentially at each frame?
============ command 1: view view_a 4 #### transit to view_a
in 4 frames/steps
command 2: transparency #1 50 target s #### on frame 1 command 3: color # 2 magenta target c #### on frame 2 command 4: display #1/A:10 #### on frame 3 command 5: transparency #3 20 target c #### on frame 4 ============ Steve
On Thu, Feb 21, 2019 at 11:15 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, You can use other commands with frame arguments (perframe, etc.) to do
other things at the same time as the movement transitions. In a command file, if you put multiple commands on the same line separated by semicolons (and no “wait” command between), they start executing at the same time.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html
See the general information about making movies http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
…and scripting with command files <
http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-f...
To divide into more positioning stages, you would have to save more
views at the intermediate positions. Each transition would still be pairwise between two views.
In Chimera we had “scenes” that included not only position but also
display styles and colors, and transitions between scenes, but they are not currently available in ChimeraX.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 6:04 AM, Steve Chou stevezchou@gmail.com wrote:
Thanks Elaine! This is exactly what I want.
# save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it
possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step?
Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, Not sure if it will solve the problem, but you could try saving views
(“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions.
Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com
wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot
through a straight line. If it's not, it's really difficult to get there through a straight line.
I tried something like this in a "movie" script, but it's still not
straight.
========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view
through a straight line.
Steve
Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Works for me in 0.8 and current daily build — probably you need to get a newer version of ChimeraX.
That is the first thing to check if you find discrepancies with the online documentation. Then if you still have the problem and think it’s a bug, use menu: Help… Report a Bug.
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 23, 2019, at 1:46 PM, Steve Chou stevezchou@gmail.com wrote:
It seems that "view" info is not saved in .cxs file. After I save the session, and open it the next time, 'view list' says 'No named views'. Steve
On Thu, Feb 21, 2019 at 2:18 PM Elaine Meng meng@cgl.ucsf.edu wrote: Probably. Just read the provided information about command files and making movies (links in my previous reply) including links from those pages to example movie files and tutorials, and experiment with executing your file containing some combination of action commands and “wait” commands to delay when the action commands start.
Whenever I make a script it involves a lot of trial and error, (re)executing the script and adjusting it. Just try it rather than asking here about each detail in your movie.
I suspect you will really be using much larger frame numbers, as 4 frames will happen in the blink of an eye. The “making movies” page has a discussion of frame rate at the bottom. Elaine
On Feb 21, 2019, at 9:38 AM, Steve Chou stevezchou@gmail.com wrote:
Hi Elaine, It looks like 'perframe' command allows me to execute multiple commands at the same time. Is it possible to run one command for 4 frames, and the other 4 commands sequentially at each frame? ============ command 1: view view_a 4 #### transit to view_a in 4 frames/steps command 2: transparency #1 50 target s #### on frame 1 command 3: color # 2 magenta target c #### on frame 2 command 4: display #1/A:10 #### on frame 3 command 5: transparency #3 20 target c #### on frame 4 ============ Steve
On Thu, Feb 21, 2019 at 11:15 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, You can use other commands with frame arguments (perframe, etc.) to do other things at the same time as the movement transitions. In a command file, if you put multiple commands on the same line separated by semicolons (and no “wait” command between), they start executing at the same time. http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html
See the general information about making movies http://rbvi.ucsf.edu/chimerax/docs/user/movies.html
…and scripting with command files http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-files
To divide into more positioning stages, you would have to save more views at the intermediate positions. Each transition would still be pairwise between two views.
In Chimera we had “scenes” that included not only position but also display styles and colors, and transitions between scenes, but they are not currently available in ChimeraX. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2019, at 6:04 AM, Steve Chou stevezchou@gmail.com wrote:
Thanks Elaine! This is exactly what I want.
# save current view settings view save my_view_name
# move to another position, zoom in or out, and color some residues etc
# get back to the original view in 20 frames along a STRAIGHT line view my_view_name 20 =============
In the 20 frames of transition time, I can not do anything now. Is it possible to do something during the transition, like changing the surface transparency? Can we save the view matrix, devide the transition into many steps, and do something else ( not motion-related, but coloring-related, etc) at each step? Steve
On Wed, Feb 20, 2019 at 7:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Steve, Not sure if it will solve the problem, but you could try saving views (“view save”) of the desired start and end positions, possibly also intermediate positions, and then use “view” with frames argument to gradually transition from one previously saved view to the another. Saved views and their names are included in saved sessions. Elaine
http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name
On Feb 20, 2019, at 4:30 PM, Steve Chou stevezchou@gmail.com wrote:
Dear ChimeraX team, Thanks for your fast and detailed responses to my questions!
If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
-
Elaine Meng -
Steve Chou