Hi Suzanne,
I'll make the guess that it's position and color. Are there any lines to be
ignored? Probably this will work anyway... Save this in a script called
holecgo.py:
def holecgo(filename,radius=0.1,name="hole"):
data = [ i.split() for i in open(filename) ]
data = [ [ float(i) for i in k[:6] ] if len(k) == 7 and
k[6].startswith("#") ]
cmd.load_cgo([u for x,y,z,r,g,b in data for u in
[6.0,r,g,b,7.0,x,y,z,radius]],name)
Then in Pymol, do:
run holecgo.py
holecgo("yourfilename")
You can add radius=0.25 or something else to make the spheres larger.
Hope it helps,
Tsjerk
On Mon, Sep 21, 2015 at 9:06 PM, Suzanne Scott <
suzanne.sc...@merton.ox.ac.uk> wrote:
> Hi everyone,
>
> I hope this isn’t a silly question, but I’m not sure how to do it: I want
> to plot some coordinates in PyMOL. Not atoms, just coordinates - they’re
> the output of HOLE implemented in Coot, and have the following format:
>
> 145.32307 113.91329 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 147.35472 113.65778 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 149.39126 113.87088 116.36907 0.44800 0.47168 0.80000
> #7278cc
> 141.61303 115.28156 115.56962 0.44800 0.47168 0.80000
> #7278cc
>
> Where the first three columns are the x, y and z coordinates, the next
> three are the size of the object, and the last is the colour (which isn’t
> so important - neither is the size, really). I can’t work out how to
> import them into PyMOL. If anybody has any ideas, I’d be really grateful!
>
> Thanks,
> Suzanne
>
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--
Tsjerk A. Wassenaar, Ph.D.
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