Dear chimera users,
I have two doubts regarding per-frame actions:
1) I am trying to add a counter in my script (commands script, no python script).
It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script:
Something like this:
movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>"
perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4
2) What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script?
Thank you very much!, Clara
Hi Clara, Since you want to do some math with the frame number, I think you’ll need to resort to Python, but since you know all the Chimera command equivalents, it won’t be that hard. The trick is to be aware that the following Python code will execute Chimera commands:
from chimera import runCommand runCommand(“some chimera command here”) runCommand(“another chimera command”)
So if you use a Python as the MD Movie per-frame script, it could be something like:
from chimera import runCommand if mdInfo[‘frame’] == 1: runCommand(“2dlabels create timer text “0 ns" size 40 color white”) else: runCommand(“2dlabels change timer text “%.2f ns” % (mdInfo[‘frame] / 1000.0))
On the first frame it creates the label, and on subsequent frames it updates the label with a 2-decimal-place floating-point number [i.e. the format “%.2f” in the string] taken from the current frame number divided by 1000. Note that indentation is significant in Python, so the runCommand statements inside the if/else have to be indented the way I’ve shown.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 26, 2019, at 6:02 AM, CLARA BLANES MIRA c.blanes@goumh.umh.es wrote:
Dear chimera users,
I have two doubts regarding per-frame actions:
- I am trying to add a counter in my script (commands script, no python script).
It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script:
Something like this:
movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>"
perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4
- What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script?
Thank you very much!, Clara
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Clara, I had a test system of model #3 trajectory with 81 frames and this script worked:
2dlabels create timer text "time = 0 ns" size 30 xpos .05 ypos .05 color black alias ^actions 2dlabels change timer text "time = $1 ns" wait 20 perframe actions; coordset #3 1,81,2; wait 40; ~perframe wait 40 2dlabels delete timer
Even though I had 81 *trajectory* frames, since coordset only showed 40 *graphics* frames, the count only goes up to 40, which is what you wanted anyway, in your situation of showing one snapshot per nanosecond. You just need to change your alias line to something like in my example. “<FRAME>” is something you can only use in the MD Movie dialog, not command scripts.
if you are showing protein ribbon and the secondary structure is changing, you may want to include ksdssp in your alias, e.g.
alias ^actions 2dlabels change timer text "time = $1 ns”; ksdssp
I think that answers your question, but I was also wondering if I could show numbering with a different start value, e.g. 41-80. This is more troublesome… although this worked to show numbering 41-80
perframe actions range 41,80; coordset #3 1,81,2; wait 40; ~perframe
...it also generated an error message that stopped the script (and thus would mess up movie recording). I guess a python script is needed to do something fancier like that.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2019, at 6:02 AM, CLARA BLANES MIRA c.blanes@goumh.umh.es wrote:
Dear chimera users,
I have two doubts regarding per-frame actions:
- I am trying to add a counter in my script (commands script, no python script).
It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script:
Something like this:
movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>"
perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4
- What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script?
Thank you very much!, Clara
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
P.S. The error on my second example with the “range” option added to shift the numbering was because I did not remove the “~perframe” at the end of the line. The ~perframe was redundant because perframe automatically stops when the end of the range is reached.
On Jun 26, 2019, at 11:22 AM, Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Clara, I had a test system of model #3 trajectory with 81 frames and this script worked:
2dlabels create timer text "time = 0 ns" size 30 xpos .05 ypos .05 color black alias ^actions 2dlabels change timer text "time = $1 ns" wait 20 perframe actions; coordset #3 1,81,2; wait 40; ~perframe wait 40 2dlabels delete timer
Even though I had 81 *trajectory* frames, since coordset only showed 40 *graphics* frames, the count only goes up to 40, which is what you wanted anyway, in your situation of showing one snapshot per nanosecond. You just need to change your alias line to something like in my example. “<FRAME>” is something you can only use in the MD Movie dialog, not command scripts.
if you are showing protein ribbon and the secondary structure is changing, you may want to include ksdssp in your alias, e.g.
alias ^actions 2dlabels change timer text "time = $1 ns”; ksdssp
I think that answers your question, but I was also wondering if I could show numbering with a different start value, e.g. 41-80. This is more troublesome… although this worked to show numbering 41-80
perframe actions range 41,80; coordset #3 1,81,2; wait 40; ~perframe
Should be:
perframe actions range 41,80; coordset #3 1,81,2; wait 40
...it also generated an error message that stopped the script (and thus would mess up movie recording). I guess a python script is needed to do something fancier like that.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 26, 2019, at 6:02 AM, CLARA BLANES MIRA c.blanes@goumh.umh.es wrote:
Dear chimera users,
I have two doubts regarding per-frame actions:
- I am trying to add a counter in my script (commands script, no python script).
It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script:
Something like this:
movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>"
perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4
- What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script?
Thank you very much!,
One more suggestion about how to convert frame numbers to seconds in the perframe command for showing a label. You can use the perframe "range" option with floating point values, for example,
perframe "echo $1" range 0,0.4 frames 11
0 0.04 0.08 0.12 0.16 0.2 0.24 0.28 0.32 0.36 0.4
So you would use the range option to specify the time interval corresponding to the specified number of frames (minus one).
tom
On Jun 26, 2019, at 6:02 AM, CLARA BLANES MIRA c.blanes@goumh.umh.es wrote:
Dear chimera users,
I have two doubts regarding per-frame actions:
- I am trying to add a counter in my script (commands script, no python script).
It works when I do it as a per-frame action in the MD Movie window (just as Elaine does in the’Trajectory and ensemble Analysis Tutorial’) but I am not able to do insert it in my command script:
Something like this:
movie record 2dlabels create timer text “frame 0" size 40 color white alias ^actions 2dlabels change timer text "frame <FRAME>"
perframe actions; coordset #0 1,216000,1000 load false; wait 216; ~perframe movie encode movie.mp4
- What I really want is to show nanoseconds, not frames. In my case 1000 frames = 1 ns. When I write frame <FRAME>/1000 in MD Movie window, obviously, it does not work. Any suggestion to make it work and insert it in the commands script?
Thank you very much!, Clara
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
CLARA BLANES MIRA -
Elaine Meng -
Eric Pettersen -
Tom Goddard