[Chimera-users] pseudo bond reader in command line

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 4 14:27:33 PST 2013

Hi Beth,
If I understand correctly it sounds doable, since you can use "movie record" to start recording and "movie stop" to start recording multiple times before encoding all those saved frames with  "movie encode."   

It ultimately depends on the actual content you plan for your movie:  whether you can do all the things you want to do via Chimera commands, both during the recording and for the setup in between.   You could probably do a lot of the setup at the beginning, but I don't see any reason not to break up the recording steps, especially if it makes sense to you when writing your script.

Your description included the word "scene," but I couldn't tell if you were just referring to those in the dictionary sense, or actually to Chimera "scenes," which are a specific thing.  We have a new Animation tool, which in Chimera 1.7 and newer includes a timeline along which you can place saved scenes to define your movie content.  However, it is still under development.  It completely depends on what you will be showing as to whether this would work better than your script approach.  It will automatically interpolate colors, for example, which is not really doable in a Chimera script, but the universe of things that can be done and the amount of control over content is greater using a Chimera script than using the current Animation tool.  This tool is meant to be a friendly graphical interface to decrease the learning curve for people who want to create movies containing common operations like rotating and zooming.

Making movies in Chimera (overview of approaches):

Chimera scenes:

Animation tool:

You may want to take a look, but I have no reason to doubt your current approach is fine for what you have in mind.  Best,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 4, 2013, at 12:46 PM, M. Elizabeth Stroupe wrote:

> Yes - that helps a lot.  I think option B will be best.
> I think this will get me the panels I need to make the movie….I may need some more guidance to put it all together, though!
> My strategy is to build a scene, then record some frames, then build the next scene, then record frames (for at least 5 panels).  Can I do this in one script by using the line command "movie"?  Is there a better way?
> Thank you so much for your quick response.
> Beth
> On Feb 4, 2013, at 2:58 PM, Elaine Meng wrote:
>> Hi Beth,
>> Although there is no command implementation of Pseudobond Reader, I think there are at least a couple ways to do what you want:
>> (A) Before running the movie script, use Pseudobond Reader, hide all the pseudobonds (and you could have a session saved at this point) and have the script re-show them.  Hiding, showing, and controlling their color and line style (e.g. dotted) can all be done with the "setattr" command.
>> (B) If you really wanted everything to be in a command script rather than an initial session, however, you could alternatively create the pseudobonds as distance monitors using the "distance" command.  As in method A, you could hide, show, and control appearance with "setattr."
>> The pseudobond group "distance monitor" and/or pseudobond group(s) created with Pseudobond Reader will be listed in the PseudoBond Panel (in menu under Tools... General Controls).  Click the group name on the left and "attributes..." on the right side of the PseudoBond Panel to see what things are available for changing with the command "setattr" -- the top section has group attributes ("g" in setattr command) and the bottom section has individual pseudobond attributes ("p") in setattr command. If you hover the mouse over something in that dialog, balloon help will show the attribute name to be used in the setattr command, as well as its possible values.
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
>> Example commands:
>> setattr g display 0
>> (hide all pseudobond groups; 0=hide 1=show)
>> setattr p display 0 #0&protein
>> (hide all pseudobonds between atoms of protein in model #0)
>> setattr p color orange sel
>> (color pseudobonds between the currently selected atoms orange)
>> setattr g lineWidth 3
>> setattr g lineType 2
>> (make all pseudobond groups use line width 3, dashed lines)
>> setattr p label " "
>> (replace distance monitor labels with blank... although the label attribute is not listed in the attributes panel opened from PseudoBond Panel, it is in the Selection Inspector, for example if you Ctrl-click to select a pseudobond and then click the green magnifying glass).
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Feb 4, 2013, at 11:27 AM, M. Elizabeth Stroupe wrote:
>>> Hi,
>>> I am trying to make a figure with pseudo bonds - the figure is fairly complicated and it will be a frame in a movie of related shots, so I need to call the pseudo bonds in from the command line.
>>> How do I read in a text file that defines the pseudo bonds (as if from the pseudo bond reader) and then alter their attributes (to make them into dotted rather solid lines)?
>>> Thanks much,
>>> Beth
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