Hi Gesa, The first thing to check is whether the ligand is hidden when you just open the session without doing anything else. The second thing is that there should probably be a wait after the fly command, at least if you want the fly to finish before subsequent commands are executed. But see the next point... In older versions of Chimera (before 1.5.3), it was necessary to put the same number of frames used in the fly command in the subsequent wait command, fly 80 view_hoch view_quer wait 80 To avoid this third issue, it would be better to use Chimera 1.5.3 or newer. I hope this helps, Elaine On Sep 1, 2011, at 11:38 AM, Gesa Volkers wrote:

Dear Elaine,

thank you, roundtrip was the key.

Now I encountered another problem in my movie script. I wish to display a ligand in the movie AFTER I moved, rolled and rocked my molecule. But the ligand appears right in the beginning and then the molecule starts moving, rotating, rocking and so on. My script commands are:

open ...\surface_preset.py movie record fformat png supersample 3 fly 80 view_hoch view_quer roll x 1 450 wait rock y 4 136 wait color yellow #0:391 wait color byhetero #0:391 wait display #0:391 wait [...]

Can you point me towards the mistake in my scripting commands? Thank you again for your patience.

Gesa

Am 01.09.2011 19:49, schrieb Elaine Meng:

...

Dear Gesa, Your old sessions should be fine in newer Chimera -- if not, you could try using Help... Report a Bug in the Chimera menu and attach the session file and describe what the problem is. It is the opposite situation that might cause problems, i.e. old Chimera with a session made with newer Chimera.

The movie command has all the same options as the dialog, so in a command file you would use those command options instead of dialog settings. Here is the manual page,

<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>

which shows that the "movie encode" option "roundtrip" is the setting you want.

With the movie command, the syntax is like "supersample N". Supersampling will not make the movie file any bigger because each image still ends up the same size. Supersampling just means a bigger image is made first and then sampled down to the final size. I just now tried making movies with supersampling 3 and no supersamping and the difference is rather subtle. Without supersampling you can see a little bit of jaggedness along the edge of ribbons and sticks. I think 4 is overkill. The quality reduction during movie encoding (which has some compression) probably swamps out most of the supersampling, and although I usually recommend 3 for saving single images, it is a less dramatic improvement for movies.

I hope this helps. Thanks for the compliments, by the way! Elaine

On Sep 1, 2011, at 9:57 AM, Gesa Volkers wrote:

...

Dear Chimera-Programmers,

I like to create a movie in chimera by using a txt script and have some questions.

I saw that it is possible to check the box "play forward then backward" in the movie recorder but it does not work when I check the box and then run my script to create the movie (maybe this is not suprising..). How can I include this command into my script commands?

Another question. If I use the supersampling command, is it right to use the command as follows:

movie record fformat png supersample 4

OR

movie record fformat png supersample 4x4

Somehow I cannot see a difference in quality if I use the supersample command like this or if I do not use it at all, so I assume that something is wrong. Also the mp4-file size is always the same.

And a third question: I liked to upgrade Chimera to the current version (I use 1.5 (build 31025) 2010-07-20). But after the upgrade all my old saved sessions did not work anymore. Is there a solution for this? Because that keeps me from upgrading..

Thank you in advance for your help! I use Chimera a lot and I am always surprised how helpful the tutorials are and how fast the programmers respond to the users.

Gesa