Step through trajectory from command line?
Hi- Can you advance a trajectory by one frame from the command line, or do you have to use the controls in the MD Movie panel? Thanks, Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904
Hi Kristina, There is no command for advancing trajectory frames. Perhaps you can detail the scenario that you need this for and why the per-frame scripting of the MD Movie tool doesn't cover your needs. Are you trying to completely automate the production of a movie from a trajectory or some such? Even if there were a command to advance the trajectory, how would you know when to stop? There are no "flow control" statements (if statements/for loops/functions) in the Chimera command language. I think you will have to use Python scripting for completely automating trajectory-related scripting. I can provide assistance there. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 29, 2008, at 10:18 AM, Kristina Furse wrote:
Hi-
Can you advance a trajectory by one frame from the command line, or do you have to use the controls in the MD Movie panel?
Thanks, Kristina
-- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
There is no command for advancing trajectory frames. Perhaps you can detail the scenario that you need this for and why the per-frame scripting of the MD Movie tool doesn't cover your needs. Are you trying to completely automate the production of a movie from a trajectory or some such?
Yes.
Even if there were a command to advance the trajectory, how would you know when to stop? There are no "flow control" statements (if statements/for loops/functions) in the Chimera command language. I think you will have to use Python scripting for completely automating trajectory-related scripting. I can provide assistance there.
You are correct in your assessment--I don't know Python, but I do know Perl so I just wanted to use Perl to produce a line by line Chimera script that would do some zooms and rotations, writing POV files (actually x3d files that I'll translate into POV files in a later step), then flow straight into an MD movie, writing POV files for each frame. No worries--I'm sure I can figure out how to do a per-frame Python script that will write an x3d file with a unique name for each trajectory frame. It just made more sense to me the other way around. Thanks! Kristina -- Kristina Furse Postdoctoral Research Associate 262 Stepan Chemistry Hall Notre Dame, IN 46556 (574)631-3904
On Mar 5, 2008, at 8:28 AM, Kristina Furse wrote:
You are correct in your assessment--I don't know Python, but I do know Perl so I just wanted to use Perl to produce a line by line Chimera script that would do some zooms and rotations, writing POV files (actually x3d files that I'll translate into POV files in a later step), then flow straight into an MD movie, writing POV files for each frame. No worries--I'm sure I can figure out how to do a per-frame Python script that will write an x3d file with a unique name for each trajectory frame. It just made more sense to me the other way around.
Unless you are going to process many trajectories, the easiest approach I think is for you to write your Perl script to handle the initial zoom/rotation part, then to switch to MD Movie's per-frame scripting for the rest. You don't have to use Python for the per- frame scripting, you can use regular Chimera commands. As mentioned in the per-frame dialog, the string "<FRAME>" in commands will be substituted with the current frame number, so it should be easy to produce uniquely-named files. --Eric
participants (2)
-
Eric Pettersen -
Kristina Furse