David wrote:
How do I access the objects I load from files (e.g. pdb file) directly
(i.e. in a script)? If I want to print the coordinates of an atom, or
the value of at a point in the electron density grid?
http://www.rubor.de/bioinf/pymol_tips.html#getcoord
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Eric Hu wrote:
>Hi, I wonder if anyone has had the similar problem. I
>can see both the label and dash at normal window.
>After raytracing there is only a yellow dotted line
>between two atoms without the distance. How can I make
>the distance shown on the raytracing picture? Thanks!
As far as i know, the only way is to use CGO-Text for labels. This is
tough, though.
http://www.rubor.de/bioinf/pymol_tips.html#cgolabels
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Fei Xu wrote:
>Would you like to tell me what kind of commands I can use to draw a line
>in pymol, if I know the exact location of this line in 3D-space?
You can use CGO objects from a python script like this:
# cgo-example.py
from pymol import cmd
from pymol.cgo import *
obj = [CYLINDER, 0.1, 0.1, 0.1, 10.0, 0.0, 0.0, 0.1, 0.0, 0.0, 1.0, 1.0,
0.0, 0.5,]
cmd.load_cgo(obj,'hbonds')
The values in the obj array are: [CYLINDER, start_position X,Y,Z,
end_position X,Y,Z, thickness, unknown, color
pos1 xyz, pos2 xyz, thick, start_color R,G,B, end_color R,G,B]
Happy New Year!
Kristian Rother
