1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script. 2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where & when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command. 3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing. 4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code. 5) I prefer to keep up with the daily builds & submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk. thanks for the good product. Matthew Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine
Hi Matt, Those are all good suggestions. I'll talk to Darren, our animation programmer, and perhaps he or I can work on some of them. I could see request 2 perhaps being combined with 1. You could put in a pause script command which would then show a dialog that would allow you to continue or single step frame by frame from that point on. It could single step through any transition, not just reset command motions. It would be limited in that it wouldn't allow backing up, and might not allow you to use any other Chimera menu or mouse operation -- it would just be frozen, with the options to play a single frame, or to resume continuous playback. The single stepping combined with your frame count stamp (request 3) would allow identifying exactly where to insert an extra keyframe to avoid a collision between molecules. There is a solution for request 5 already. Of course, you don't want to reinstall a bunch of plug-ins not included in the distribution every time you update. To avoid this make a directory, called for example chimera-plugins, that is outside of the Chimera distribution directory. Install the plugins in that directory and use Favorites / Preferences / Category Tools and add the chimera-plugins directory to the Tool Locations using the Add... button at the bottom. Press the Save button so that setting is saved in your Chimera preferences. Installing a new Chimera version uses your existing preferences, so all your plugins will still work in the new Chimera with no extra fuss. Tom
1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script.
2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where& when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command.
3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing.
4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code.
5) I prefer to keep up with the daily builds& submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk.
thanks for the good product.
Matthew
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine
Hi Matt, A few comments on your issues #1 and #3: (1) Command script execution can be aborted by pressing the Esc (escape) key, or paused/resumed with Shift-Esc. There is also a "pause" command, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html> after which you could resume executing the script by pressing any key other than Esc or End, or abort execution by pressing End. (3) I'm thinking it can be done with the commands "perframe" "alias" and "2dlabels" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> e.g. open 2gbp 2dlab create count xpos .05 ypos .05 alias ^framecount 2dlab change count text $1 color orange perframe framecount 3; roll y 1 90; wait; ~perframe I'm not sure how to exactly synchronize that with the start of movie recording, however. Maybe it would do that if the movie record command was right before the perframe command in the same line, separated by semicolon. Also, of course this is not as convenient as an automatic built-in counter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 18, 2011, at 12:21 AM, Dougherty, Matthew T wrote:
1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script.
2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where & when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command.
3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing.
4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code.
5) I prefer to keep up with the daily builds & submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk.
thanks for the good product.
Matthew
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine & Tom, Is there a way to issue the escape key within a script? I thought of another suggestion: 6) Just like overwriting a file, a dialog comes up to verify the overwrite or an command option to ignore in a write script command; something similar for savepos would prevent a lot of missteps. For example, when I have two session files I am merging, the second session clobbers the first session keyframe names if they are identical, which may or may not be desirable. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, February 18, 2011 1:25 PM To: Dougherty, Matthew T Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] animation suggestions Hi Matt, A few comments on your issues #1 and #3: (1) Command script execution can be aborted by pressing the Esc (escape) key, or paused/resumed with Shift-Esc. There is also a "pause" command, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html> after which you could resume executing the script by pressing any key other than Esc or End, or abort execution by pressing End. (3) I'm thinking it can be done with the commands "perframe" "alias" and "2dlabels" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html> e.g. open 2gbp 2dlab create count xpos .05 ypos .05 alias ^framecount 2dlab change count text $1 color orange perframe framecount 3; roll y 1 90; wait; ~perframe I'm not sure how to exactly synchronize that with the start of movie recording, however. Maybe it would do that if the movie record command was right before the perframe command in the same line, separated by semicolon. Also, of course this is not as convenient as an automatic built-in counter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Feb 18, 2011, at 12:21 AM, Dougherty, Matthew T wrote:
1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script.
2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where & when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command.
3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing.
4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code.
5) I prefer to keep up with the daily builds & submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk.
thanks for the good product.
Matthew
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Matt, Doesn't the "pause" command do essentially the same thing as issuing an escape key in a script? I wasn't familiar with the "pause" command before Elaine mentioned it in the preceding email. Tom
Thanks Elaine& Tom,
Is there a way to issue the escape key within a script?
I thought of another suggestion:
6) Just like overwriting a file, a dialog comes up to verify the overwrite or an command option to ignore in a write script command; something similar for savepos would prevent a lot of missteps. For example, when I have two session files I am merging, the second session clobbers the first session keyframe names if they are identical, which may or may not be desirable.
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, February 18, 2011 1:25 PM To: Dougherty, Matthew T Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] animation suggestions
Hi Matt, A few comments on your issues #1 and #3:
(1) Command script execution can be aborted by pressing the Esc (escape) key, or paused/resumed with Shift-Esc. There is also a "pause" command,
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/pause.html>
after which you could resume executing the script by pressing any key other than Esc or End, or abort execution by pressing End.
(3) I'm thinking it can be done with the commands "perframe" "alias" and "2dlabels" <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/2dlabels.html>
e.g. open 2gbp 2dlab create count xpos .05 ypos .05 alias ^framecount 2dlab change count text $1 color orange perframe framecount 3; roll y 1 90; wait; ~perframe
I'm not sure how to exactly synchronize that with the start of movie recording, however. Maybe it would do that if the movie record command was right before the perframe command in the same line, separated by semicolon. Also, of course this is not as convenient as an automatic built-in counter.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 18, 2011, at 12:21 AM, Dougherty, Matthew T wrote:
1) It would be helpful for debugging to have script command that would halt scripting, after which a dialog box or a keyboard command could continue or restart the script.
2) sometimes when doing a reset command (e.g. kf1 to kf2) the trajectory crashes through something in the middle, so another intermediate keyframe (e.g., kf1.1) has to be created to dodge flying through an atom, requiring two reset commands to get from kf1 to kf2. Figuring out where& when kf1.1 should be placed is problematic. It would be helpful to have a debug mode that would allow stepping through the individual frames of a reset command.
3) having a optional frame count stamped on the images would be helpful for debug and non-linear editing.
4) sometimes using an icosahedron to start off a virus animation is preferred, particularly a wireframe icos. Having the ability to adjust the diameter of the line is which, which can be done in an obscure way. Being able to adjust it as a slider from the icos panel would be easier, and being able to dynamically change it through script interpolation would be a good addition to the animation commands in the experimental code.
5) I prefer to keep up with the daily builds& submitting bug reports. The inertia is having to reinstall the animation commands and other plug-ins from the experimental code every time on different computers. Having a more automated way within chimera to include these packages (user developed plugins) during installation of chimera, like a checkbox list that automatically pulls the plugins off the website or local disk.
thanks for the good product.
Matthew
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Dougherty, Matthew T -
Elaine Meng -
Tom Goddard