Re: [PyMOL] recent problems

[Kristian R. <kri...@be...>]

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

----------------

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

--------------

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