[Chimera-users] pseudo bond reader in command line

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 4 11:58:29 PST 2013

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.

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 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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