Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in? Thanks Dan ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon@depauw.edu
Hi Daniel, The demo capability in Chimera is designed to do what you want including rewind. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html It doesn't allow pausing in the middle of a motion -- only between panels (maybe between individual commands associated with a panel - not sure). But the idea is that the duration of motion in each panel would be short. We haven't made many demos and this tool may be pretty rough around the edges. The trouble with the pause command or Shift-Escape to pause/resume a script is that the fly command returns immediately after you invoke it. It sets up playing the motion which then happens after the command returns. Normally that motion could be halted with the command "freeze". This works with other motion commands "reset", "roll", "move", and it should work with "fly" but doesn't yet work for "fly". In any case, it simply terminates the motion and there is no way to restart it, so that won't do what you want. There is no mechanism to pause the playback in these motion commands, though maybe "pause" and the Shift-Escape key should be made to do that. Currently those mechanisms just block running of additional commands I believe. I wonder whether pause/resume would be adequate for teaching purposes. Seems very likely to me that you will need rewind. By the time a student asks a question the motion is already past the relevant section. We don't have any rewind capability in the motion commands or in general scripts, only the demo tool, and even there I think can be tricky to make it work. Tom -------- Original Message -------- Subject: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: chimera-users@cgl.ucsf.edu Date: 8/21/09 5:52 PM
Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in?
Thanks Dan
____________________________
Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135
Hi Daniel, You might consider writing your script with a series of "reset" commands rather than "fly" -- the difference is that fly considers the trajectory to be taken after the next position, so that the whole thing looks smoother. If A,B,C,D are saved positions, schematically: fly A -> B -> C -> D where the approach to C is already being considered before arriving at B, versus reset -> A; wait reset -> B; wait ... where each reset command can specify number of frames (does not have to be instantaneous) The wait commands prevent the movement commands from overlapping execution. Shift-Esc will pause the script after the current command is done. If it is in the middle of a reset to C, it will go that far and then stop at C. Then it can be resumed with another Shift-Esc. That is not as precise as what you had asked about (instantaneously pausing), but more precise than after an entire fly command finishes. A demo is inherently a series of commands, and doesn't allow pausing in the middle of a command, so "reset" is probably also needed in that case. It is the only way I can think of in Chimera where you can just press a button to go back to a previous state. Easy for the user, but... Demo issues: - you would need to start the demo by opening a session with your saved positions, unless you know how to generate those positions by a series of commands - the "go back" feature automatically takes care of positions, but the demo creator is responsible for figuring out any other commands needed to revert to the previous state (any displaying/undisplaying, changing colors, styles). It can be more confusing than it sounds! You can see the "guts" of a demo by choosing it from the Tools... Demos menu (starting to play it back) but then choosing "File... Open in Editor" from the demo panel. Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 21, 2009, at 6:25 PM, Tom Goddard wrote:
Hi Daniel,
The demo capability in Chimera is designed to do what you want including rewind.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/ demos.html
It doesn't allow pausing in the middle of a motion -- only between panels (maybe between individual commands associated with a panel - not sure). But the idea is that the duration of motion in each panel would be short. We haven't made many demos and this tool may be pretty rough around the edges.
The trouble with the pause command or Shift-Escape to pause/resume a script is that the fly command returns immediately after you invoke it. It sets up playing the motion which then happens after the command returns. Normally that motion could be halted with the command "freeze". This works with other motion commands "reset", "roll", "move", and it should work with "fly" but doesn't yet work for "fly". In any case, it simply terminates the motion and there is no way to restart it, so that won't do what you want. There is no mechanism to pause the playback in these motion commands, though maybe "pause" and the Shift-Escape key should be made to do that. Currently those mechanisms just block running of additional commands I believe.
I wonder whether pause/resume would be adequate for teaching purposes. Seems very likely to me that you will need rewind. By the time a student asks a question the motion is already past the relevant section. We don't have any rewind capability in the motion commands or in general scripts, only the demo tool, and even there I think can be tricky to make it work.
Tom
-------- Original Message -------- Subject: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: chimera-users@cgl.ucsf.edu Date: 8/21/09 5:52 PM
Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in?
Thanks Dan
____________________________
Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Dan, If you haven't already, you should check out the two demos (cox inhibitors, hormone-receptor complex) in the Chimera Tools / Demos menu. These were made by Elaine Meng. If you look at pane 7 of the cox demo there are some html-style links "sticks" and "spheres" that allow you to change rendering options. You can also use the normal Chimera menus and tinker with the rendering and view point and the demo will usually revert to the normal depiction when you go to the next pane. Whether it does or not depends on how thorough the commands that define the demo are about setting all the display styles in case the user has fiddled. Going from panes 4 to 5 there is some motion of the molecules. But then pressing the back button jumps immediately to the preceding positions -- it does not show the motion in reverse. It may be easy to make the back button reverse the motion. In general the back operation has to be given as a series of commands that the demo creator knows will undo the forward step. You could put in the backwards motion commands. I have never made a demo so I am guessing. We are interested in improving Chimera for interactive teaching. Our thinking when developing the demo editor was more geared towards showing a researcher new to Chimera some of the Chimera capabilities. Creating these demos does not require programming knowledge, but rather a good knowledge of the Chimera commands. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html Before you team up with some computer science people, I think the steps should be: 1) study the two demos included in Chimera, and the commands used in those demos, 2) try making a simple demo from your own material, 3) talk with us about the problems you find. I think you'll encounter two problems, first that some needed commands don't exist, and second that the demo editor and player are clunky (it hasn't been used much to our knowledge). Both of these things we can work with you to improve -- possibly with pretty quick turn-around time (days/weeks). Tom -------- Original Message -------- Subject: Re: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: goddard@cgl.ucsf.edu Date: 8/22/09 9:24 AM
Thanks Tom. I'll try making some demos. From the ones I've seen, rewinding the demo is more like "reset", i.e., any motion won't be reversed but instead the model(s) will be reset to their position and rendering from the previous step. But it should provide much of what I need.
Over the past few months, I've been learning Autodesk Maya and talking with Gael McGill and some of the others out there that do molecular animation. While I think animation software like Maya can be a very powerful teaching tool (especially when you need to model things for which there is no 3D data set), the finished movies lack interactivity. Ideally I want modules that automate some of the learning experience (fetching a structure, rendering to highlight appropriate features, taking the viewer on a fly-by tour of the system) while also leaving the participant free to pause and explore the scene on their own. The demos in Chimera are pretty close to what I want actually, but there are a few things I'd change if I could...motion rewinding is one, but it would also be useful to add buttons enabling the user to change rendering options at each demo stop-point without the risk of screwing up the rest of the demo. It would also be nice to instantly reset the demo to the current point if you made a change you want to undo. In a nutshell, I want to design modules that any student or any teacher could use with minimal time invested in learning Chimera. I really think Chimera has a lot of potential for teaching, but the learning curve associated with the program makes it tough for the inexperienced to get the most out of the Chimera's interactive capabilities.
Do you think it would be feasible (and a good idea) for me to team up with some computer scientists at my school and work on retooling the demo editor with the goal of designing several student-friendly, interactive modules? I have a lot of experience with teaching, but none with programming, so I know what I want...I just don't know if it's possible. Any advice you can offer is much appreciated!
Dan
-------- Original Message -------- Subject: Re: [Chimera-users] pause during a fly-by? From: Tom Goddard <goddard@cgl.ucsf.edu> To: Daniel Gurnon Date: 8/21/09 6:25 PM
Hi Daniel,
The demo capability in Chimera is designed to do what you want including rewind.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html
It doesn't allow pausing in the middle of a motion -- only between panels (maybe between individual commands associated with a panel - not sure). But the idea is that the duration of motion in each panel would be short. We haven't made many demos and this tool may be pretty rough around the edges.
The trouble with the pause command or Shift-Escape to pause/resume a script is that the fly command returns immediately after you invoke it. It sets up playing the motion which then happens after the command returns. Normally that motion could be halted with the command "freeze". This works with other motion commands "reset", "roll", "move", and it should work with "fly" but doesn't yet work for "fly". In any case, it simply terminates the motion and there is no way to restart it, so that won't do what you want. There is no mechanism to pause the playback in these motion commands, though maybe "pause" and the Shift-Escape key should be made to do that. Currently those mechanisms just block running of additional commands I believe.
I wonder whether pause/resume would be adequate for teaching purposes. Seems very likely to me that you will need rewind. By the time a student asks a question the motion is already past the relevant section. We don't have any rewind capability in the motion commands or in general scripts, only the demo tool, and even there I think can be tricky to make it work.
Tom
-------- Original Message -------- Subject: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: chimera-users@cgl.ucsf.edu Date: 8/21/09 5:52 PM
Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in?
Thanks Dan
____________________________
Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135
Hello, In case it may be helpful, here is my general workflow in making the Demos distributed with Chimera (in the Tools... Demos menu): - create a Chimera command script for the whole forward process. I just create it in a text editor and then keep opening it over and over after making adjustments. I find this to be much easier than trying to use the Demo Editor at this stage. Remember to use "wait" to prevent overlapping execution of movement commands. Sometimes overlapping execution is OK, but in my experience it sometimes leads to different resulting positions on different runs of the same script. - decide which commands to string together in single lines, separated by semicolons (to avoid displaying the intermediate states, since the display just gets updated at the end of a line). This is really done in parallel with the above, so I'm still text-editing that Chimera command file. - decide how to chunk it up into panels, then enter these sets of commands in the Demo Editor, as well as the accompanying text that will show up in the Demo dialog. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/ demos.html#editor> - figure out and enter "undo" commands for each panel. You only have to do this if you want the Back button to work. - add any fancy extras such as links that execute commands (like the options to show as sticks or spheres, or show residues from just one protein or another in the COX demo). Sometimes it can be a challenge to make sure the "undo" commands will work no matter which of these things the user chooses to execute. I'm sure there are other equally valid but different ways to go about this, so feel free to choose your own path! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
participants (3)
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Daniel Gurnon -
Elaine Meng -
Tom Goddard