Hi Jean-Paul, The script you sent works for me with Mac X11 Chimera 1.2540 on Mac OS 10.4.11. I open two maps and the resulting movie is correct. You don't have any motion going on like a "roll" do you? Because the first line of this script "wait" with no frame count means that subsequent lines of the script will not be executed until all motion ceases. Likewise you have wait command with no frame count on the first two transparency setting lines. Tom Jean-Paul Armache wrote:
Thank you for the reply. It seems that I have today a lot of questions. There is one more: I have a script. When not in movie recording mode, it works fine. However, if I input movie record and at the end movie stop and encode, then at some point the script stops. Once it stopped with the labels, so at the end I removed the labels. Now I have one map visible and I want it to slowly get transparent to a point when it is no longer visible. And here lies the problem. The script is fairly easy:
wait; movie record directory /Users/jean-paularmache/tmp-chimera;
volume #1 transparency 0.0; wait; volume #0 transparency 0.0; wait;
volume #0 transparency 0.05; wait 3; volume #0 transparency 0.1; wait 3; volume #0 transparency 0.15; wait 3; volume #0 transparency 0.2; wait 3; volume #0 transparency 0.25; wait 3; volume #0 transparency 0.3; wait 3; volume #0 transparency 0.35; wait 3; volume #0 transparency 0.4; wait 3; volume #0 transparency 0.45; wait 3; volume #0 transparency 0.5; wait 3; volume #0 transparency 0.55; wait 3; volume #0 transparency 0.6; wait 3; volume #0 transparency 0.65; wait 3; volume #0 transparency 0.7; wait 3; volume #0 transparency 0.75; wait 3; volume #0 transparency 0.8; wait 3; volume #0 transparency 0.85; wait 3; volume #0 transparency 0.9; wait 3; volume #0 transparency 0.95; wait 3; volume #0 transparency 1.0; wait 3;
#movie finished movie stop; movie encode bitrate 12000 mformat avi output /Users/jean-paularmache/Desktop/firstmovie.avi
Ok, what happens is that Chimera generates endless amount of images. Really, without cease. Now, if I do "movie stop;" from the command line, it generates the avi file. However, the whole avi file consists of one frame movie (meaning that even though it has the right amount of frames, all are just one frame). What is more surprising is that with other scripts this transparency works. It is just right here that it doesn't want to cooperate. Could you think of any reasons it might be behaving like that?
Best regards,
Jean-Paul Armache
Hi Jean-Paul, It also works for me on Mac OS 10.5.4 / X11 (of course, using a different directory and output location). I get 60 frames in PPM format and the movie file. Besides what Tom said about the "wait" at the beginning, some other things to check: - are you using a recent version of Chimera? Tom and I are using releases from this month. - it's probably the e-mail software's fault for breaking it up, but the entire "movie encode" command should be one line - it is not necessary to put ";" at the end of each line... that is only needed as a separator, between commands that are on the same line. However, I tried the script both with and without all the end- of-line ";" and it did not seem to make any difference (for example, "movie stop" instead of "movie stop;") - your bitrate is extra-high - did you try just using the default? Or did this high value work in other movies? Also, I don't think we have heard of a script stopping unless there is some error in a command. In that case, however, there should be some error message in Chimera. Elaine On Jul 21, 2008, at 8:32 PM, Tom Goddard wrote:
Hi Jean-Paul,
The script you sent works for me with Mac X11 Chimera 1.2540 on Mac OS 10.4.11. I open two maps and the resulting movie is correct.
You don't have any motion going on like a "roll" do you? Because the first line of this script "wait" with no frame count means that subsequent lines of the script will not be executed until all motion ceases. Likewise you have wait command with no frame count on the first two transparency setting lines.
Tom
Jean-Paul Armache wrote:
Thank you for the reply. It seems that I have today a lot of questions. There is one more: I have a script. When not in movie recording mode, it works fine. However, if I input movie record and at the end movie stop and encode, then at some point the script stops. Once it stopped with the labels, so at the end I removed the labels. Now I have one map visible and I want it to slowly get transparent to a point when it is no longer visible. And here lies the problem. The script is fairly easy:
wait; movie record directory /Users/jean-paularmache/tmp-chimera;
volume #1 transparency 0.0; wait; volume #0 transparency 0.0; wait;
volume #0 transparency 0.05; wait 3; volume #0 transparency 0.1; wait 3; volume #0 transparency 0.15; wait 3; volume #0 transparency 0.2; wait 3; volume #0 transparency 0.25; wait 3; volume #0 transparency 0.3; wait 3; volume #0 transparency 0.35; wait 3; volume #0 transparency 0.4; wait 3; volume #0 transparency 0.45; wait 3; volume #0 transparency 0.5; wait 3; volume #0 transparency 0.55; wait 3; volume #0 transparency 0.6; wait 3; volume #0 transparency 0.65; wait 3; volume #0 transparency 0.7; wait 3; volume #0 transparency 0.75; wait 3; volume #0 transparency 0.8; wait 3; volume #0 transparency 0.85; wait 3; volume #0 transparency 0.9; wait 3; volume #0 transparency 0.95; wait 3; volume #0 transparency 1.0; wait 3;
#movie finished movie stop; movie encode bitrate 12000 mformat avi output /Users/jean-paularmache/Desktop/firstmovie.avi
Ok, what happens is that Chimera generates endless amount of images. Really, without cease. Now, if I do "movie stop;" from the command line, it generates the avi file. However, the whole avi file consists of one frame movie (meaning that even though it has the right amount of frames, all are just one frame). What is more surprising is that with other scripts this transparency works. It is just right here that it doesn't want to cooperate. Could you think of any reasons it might be behaving like that?
Best regards,
Jean-Paul Armache
Hi Jean-Paul, The movie recording script you sent works correctly for me using Mac X11 Chimera 1.2540 on Mac OS 10.5.4. The recording stops and a movie is encoded and plays correctly. We will not be able to help you unless we can reproduce your problem. To reproduce it we need to know what version of Chimera you are using and what operating system, and an exact set of steps that causes the incorrect behavior. Setting transparency to 0 is not the same as displaying the volume. If the second volume has been undisplayed with "volume #1 hide" changing its transparency will not make it appear. To redisplay it you would need "volume #1 show". Tom Jean-Paul Armache wrote:
Hello,
Now I figured when it does not work for me. When I make one of the volumes disappear (#0) and want to make the other one (#1) appear instead. The second volume (#1) does not appear and the movie does not stop recording. I don't know anymore what to do.
movie record directory /Users/jean-paularmache/tmp-chimera;
volume #0 transparency 0.05; wait 3; volume #0 transparency 0.8; wait 3; volume #0 transparency 0.85; wait 3; volume #0 transparency 0.9; wait 3; volume #0 transparency 0.95; volume #0 transparency 1.0;
volume #1 transparency 0.0;
#movie finished movie stop; movie encode bitrate 12000 mformat avi output /Users/jean-paularmache/Desktop/firstmovie.avi
Best regards,
Jean-Paul Armache
Hi Jean-Paul, Your use of the wait command with no frame count in this script is not right. Wait without a frame count waits until there is no motion before going on to the next command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/wait.html So if you have motion the script will not go anywhere (until you type freeze) as you observe. If you don't have motion, each transparency change should take one frame because the volume command causes one frame to elapse (and the waits do nothing). So your problem looks like improper use of wait. Tom Jean-Paul Armache wrote:
Hello Sir,
I know about volume undisplay. I will try to tell you exactly what happens.
I have 2 pdbs loaded, they are displayed. I generated density maps from them. I keep them displayed, however, before running the script I set them to 1.0 transparency. When I start the script, the same screen stays, there is no change. There is no change in the transparency level and if I check the intermediate image files, they are all the same. Now, if I write in the command line "freeze" and "movie stop", the screen begins to change again and all the things one would like to see start to unravel. I tried both Aqua version and X11 version. I have Macbook Pro v. 2008, 2.6 GHz Intel Core Duo Penryn, 4 GB of RAM, 512 MB on the graphic card (NVIDIA). As for the software, I have the latest Leopard, 10.5.4. Below is this script that does absolutely nothing :/
movie record
volume #8 transparency 0.95 wait volume #8 transparency 0.9 wait volume #8 transparency 0.85 wait volume #8 transparency 0.8 wait volume #8 transparency 0.75 wait volume #8 transparency 0.7 wait volume #8 transparency 0.65 wait volume #8 transparency 0.6 wait volume #8 transparency 0.55 wait volume #8 transparency 0.5 wait volume #8 transparency 0.45 wait volume #8 transparency 0.4 wait volume #8 transparency 0.35 wait volume #8 transparency 0.3 wait volume #8 transparency 0.25 wait volume #8 transparency 0.2 wait volume #8 transparency 0.15 wait volume #8 transparency 0.1 wait volume #8 transparency 0.05 wait volume #8 transparency 0.0 wait
movie stop
movie encode bitrate 1200 mformat avi output /Users/jean-paularmache/Desktop/pdbs_final2.avi
Best regards,
Jean-Paul Armache
Dear Sir, Your answer has been helpful. Thank you. However.... I edited the file and did something like that movie record volume #8 transparency 0.95 wait 4 volume #8 transparency 0.9 wait 4 volume #8 transparency 0.85 wait 4 volume #8 transparency 0.8 wait 4 volume #8 transparency 0.75 wait 4 volume #8 transparency 0.7 wait 4 volume #8 transparency 0.65 wait 4 volume #8 transparency 0.6 wait 4 volume #8 transparency 0.55 wait 4 volume #8 transparency 0.5 wait 4 volume #8 transparency 0.45 wait 4 volume #8 transparency 0.4 wait 4 volume #8 transparency 0.35 wait 4 volume #8 transparency 0.3 wait 4 volume #8 transparency 0.25 wait 4 volume #8 transparency 0.2 wait 4 volume #8 transparency 0.15 wait 4 volume #8 transparency 0.1 wait 4 volume #8 transparency 0.05 wait 4 volume #8 transparency 0.0 wait 4 movie stop movie encode bitrate 1200 mformat avi output /Users/jean-paularmache/Desktop/pdbs_final2.avi with any lower or higher wait it did not function. Ok, having that I thought about doing the thing to two volumes at the same time, so I did volume #8, 9 transparency 0.95 wait 4 it did not function, therefore I changed the wait for a larger number. It did not work at all. The same problem as before. So, I did two blocks (copied the block for 8 and changed into 9) and applied the 4,5,6 etc waiting command. Nothing worked as before. However, I might have found one thing that might indicate to why it is like that. I noticed that while restoring the session, the histogram is not generated (and I work with BRIX files). To generate it and get the range, one just has to click on that file in the Volume viewer. If I don't restore the histograms, then nothing happens. If I restore the histogram for 8 and make it as a selected volume (that is selected in the Volume viewer), then the transparency steps work. However, if I restore the histogram for 8 and 9 and leave 9 as a selected volume, then nothing works. I am quite confused... :) Thank you for all the help Best regards, Jean-Paul Armache
On Jul 22, 2008, at 1:31 PM, Jean-Paul Armache wrote:
Ok, having that I thought about doing the thing to two volumes at the same time, so I did
volume #8, 9 transparency 0.95
Hi Jean-Paul, You can do more than one at a time, for example volume #8,9 transp .5 or volume #8-9 transp .5 The problem is that you put a space in the model specification. If you are not sure how to enter a command, it is better to try typing it in the command line before putting it into a script file. If you entered the command as described in your mail, there would be a message something like "Unknown option "9"" to help you realize that it is typed wrong. After you are sure your commands work, then you can worry about putting them in a file with "wait" and movie recording commands. Also, if the data is not shown at the beginning, it might work to include a command like volume #8-9 show Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Jean-Paul, Your last script works fine for me with Mac X11 Chimera 1.2540 running on Mac OS 10.4.11 where I tried a few different test volumes and "wait 2" instead of "wait 4" since you said only "wait 4" works. Either the problem depends on your computer (possibly graphics card) or more likely it depends on your exact data sets. For me to get anywhere I have to be able to make the problem happen on my machine. Since I don't have your data sets please make a demonstration script that exhibits the problem using public data. I"ve attached a script that opens an electron density server (EDS) map and does your transparency change. It works fine on my Mac OS 10.4.11 system with Radeon X1600 graphics which Chimera X11 1.2540. Perhaps you can try it and modify it as needed so it fails on your machine. Give me the exact Chimera version and graphics card and Mac OS version and a self-contained script that fails and I will see if it fails for me. If it does then I can fix it. Tom Jean-Paul Armache wrote:
Dear Sir,
Your answer has been helpful. Thank you. However....
I edited the file and did something like that
movie record
volume #8 transparency 0.95 wait 4 volume #8 transparency 0.9 wait 4 volume #8 transparency 0.85 wait 4 volume #8 transparency 0.8 wait 4 volume #8 transparency 0.75 wait 4 volume #8 transparency 0.7 wait 4 volume #8 transparency 0.65 wait 4 volume #8 transparency 0.6 wait 4 volume #8 transparency 0.55 wait 4 volume #8 transparency 0.5 wait 4 volume #8 transparency 0.45 wait 4 volume #8 transparency 0.4 wait 4 volume #8 transparency 0.35 wait 4 volume #8 transparency 0.3 wait 4 volume #8 transparency 0.25 wait 4 volume #8 transparency 0.2 wait 4 volume #8 transparency 0.15 wait 4 volume #8 transparency 0.1 wait 4 volume #8 transparency 0.05 wait 4 volume #8 transparency 0.0 wait 4
movie stop
movie encode bitrate 1200 mformat avi output /Users/jean-paularmache/Desktop/pdbs_final2.avi
with any lower or higher wait it did not function. Ok, having that I thought about doing the thing to two volumes at the same time, so I did
volume #8, 9 transparency 0.95 wait 4
it did not function, therefore I changed the wait for a larger number. It did not work at all. The same problem as before. So, I did two blocks (copied the block for 8 and changed into 9) and applied the 4,5,6 etc waiting command. Nothing worked as before.
However, I might have found one thing that might indicate to why it is like that. I noticed that while restoring the session, the histogram is not generated (and I work with BRIX files). To generate it and get the range, one just has to click on that file in the Volume viewer.
If I don't restore the histograms, then nothing happens. If I restore the histogram for 8 and make it as a selected volume (that is selected in the Volume viewer), then the transparency steps work. However, if I restore the histogram for 8 and 9 and leave 9 as a selected volume, then nothing works.
I am quite confused... :)
Thank you for all the help
Best regards,
Jean-Paul Armache _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
open edsID:1a0m movie record volume #0 transparency 0.95 wait 2 volume #0 transparency 0.9 wait 2 volume #0 transparency 0.85 wait 2 volume #0 transparency 0.8 wait 2 volume #0 transparency 0.75 wait 2 volume #0 transparency 0.7 wait 2 volume #0 transparency 0.65 wait 2 volume #0 transparency 0.6 wait 2 volume #0 transparency 0.55 wait 2 volume #0 transparency 0.5 wait 2 volume #0 transparency 0.45 wait 2 volume #0 transparency 0.4 wait 2 volume #0 transparency 0.35 wait 2 volume #0 transparency 0.3 wait 2 volume #0 transparency 0.25 wait 2 volume #0 transparency 0.2 wait 2 volume #0 transparency 0.15 wait 2 volume #0 transparency 0.1 wait 2 volume #0 transparency 0.05 wait 2 volume #0 transparency 0.0 wait 2 movie stop movie encode bitrate 1200 mformat avi output /tmp/test.avi
participants (4)
-
Elaine Meng -
Jean-Paul Armache -
Thomas Goddard -
Tom Goddard