[Chimera-users] movie panel

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 2 16:04:25 PDT 2010

Dear Susan,
It is much better to look in the User's Guide than to try to find something in the archives. Information in the User's Guide is much more complete and up-to-date, and is pretty much synchronized with your downloaded version if you access it from the Chimera Help menu.  Personally, I find it very difficult to find specific topics by searching the archive. There are copies of the User's Guide on our website, but the Help menu in Chimera connects to the copy included with your download.  So do the Help buttons on the various dialogs.  You can even search it, with "Help... Search Documentation" in the Chimera menu.

However, I understand that it can be difficult to find the answer to a seemingly simple question, so will try to answer you here... 

You can get rid of a structure by "closing" it.  In the Model Panel, on the left side you can choose the structure you want to close, and then click the "close" function on the right (*not* the Close button at the bottom which would close the Model Panel itself).  If you know the model number of that PDB, you can also just close it with a command something like "close #0".  The Command Line is shown by choosing it from the Favorites menu.

On the MD Movie dialog, if you clicked Quit it also zaps the trajectory (your morph) and you wouldn't be able to get it back.  However, if you see it still in the Model Panel, you probably clicked Hide, or maybe the dialog just got buried under other dialogs.  In that case, you can get it back to the top by choosing it from the very bottom section of the Tools menu, and then in the submenu, choose Raise.

Currently, MD Movie is not fully integrated with sessions, so you cannot get that dialog back after saving and restoring a session, sorry.  However, the whole trajectory or morph is still there and can be accessed with the "coordset" command.

The User's Guide includes several tutorials, and even more tutorials are on our website.  For example, you might want to take a look at the expanded "getting started" tutorial:

...and this animation tutorial, which includes an example of using "coordset" to play back a morph trajectory (see command file "mbp.cmd" which is linked fairly far down in the page):

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 2, 2010, at 3:23 PM, Susan Tsutakawa wrote:

> Dear Users List,
> I apologize for these novice questions.  I looked in the archives and could not find it.
> How do I get a MD molecular movement panel if I accidentally close it or I start a new session?  I made a morph and I can see it on the model panel.
> Another very novice question is how do I delete a pdb in my model panel.
> Thank you in advance.
> Sincerely,
> Susan

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