Chimera



Labels (2dlabels)


to create label lab1 containing text junk:

2dlabels create lab1 text 'junk' color light sea green 
size 26 xpos .03  ypos .92 visibility show

to modify i.e. the x and y pos of lab1:

2dlabels change lab1 xpos .13 ypos .22 visibility show

to delete label called lab1:

2dlabels delete lab1

Movies


Example of a script to create an animation that can be saved as a movie

Load pdb model, orient it and save chimera .py file.
Prepare representation of the model by using keywords as shown here:

surftransparency 50 #0;
surftransparency 50 #1;
surface #0;
surface #1;
vdwdefine 1.5 @ZN=
display @ZN=
color magenta @ZN=
ribbon #4:515-548;
color orange #4
color green #1:330-339,359-363

Now save the following as movie.com file:

surftransparency 50 #0;
surftransparency 50 #1;
surface #0;
surface #1;
vdwdefine 1.5 @ZN=
display @ZN=
color magenta @ZN=
ribbon #4:515-548;
color orange #4
color green #1:330-339,359-363
wait 100;
2dlabels create lab1 text 'the catalytic crypt of IDE' color red size 32 xpos .10  ypos .86 visibility show
2dlabels create lab2 text '~IDE-N' color blue size 26 xpos .16 ypos .22 visibility show
2dlabels create lab3 text '~IDE-C' size 26 xpos .64  ypos .22 visibility show
2dlabels create lab4 text 'hinge joining ~IDE-N and ~IDE-C' color orange size 22 xpos .65  ypos .86 visibility show
2dlabels create lab5 text 'catalytic Zinc' color magenta size 22 xpos .65  ypos .83 visibility show
2dlabels create lab6 text 'conserved exosite' color green size 22 xpos .65  ypos .80 visibility show
rock;
wait 200;
freeze;
2dlabels change lab2 visibility hide;
2dlabels change lab3 visibility hide;
roll y 2 130; wait
~surface #0;
surface #1,
2dlabels change lab2 visibility show;
rock;
wait 200;
freeze;
2dlabels change lab2 visibility hide;
surface #0;
roll y 2 90; wait
~surface #1;
2dlabels change lab3 visibility show;
rock;
wait 200;
freeze;
2dlabels change lab3 visibility hide;
surface #1;
surface #0;
roll y 2 148; wait
2dlabels change lab2 visibility show;
2dlabels change lab3 visibility show;

once the .py file is open, use the command line (Favorites>Command Line) and start the script movie.com as open movie.com
ATT. keep the window Tools>Utilities>Movie Recorder open and push Record immediately after starting the script;
the wait keywords are there to give a reasonable time interval and allow therefore to record the entire movie.

Script to generate and record simple rotation of 360 degrees

Save these lines in a file called movie.com. Open the file in chimera after the scene with the desired protein and view is set. Just opening that file will start the rotation and movie recording, and will save the movie in the same directory as spin.mov.

movie record 
turn y 3 120 
wait 120 
movie stop 
movie encode output spin.mov

By opening the "Movie Recorder" menu in Tools > Utilities, the step of the recording as from the script above can be followed, and the settings and the output can be controlled/edited.

Selections
to select residues 45-83 and 90-98 in model 3:

#3:45-83,90-98