Dear PyMOL maillist people:
I am new to mail lists. Please excuse any breaks of convention.
I suspect that a small molecule I am working with may have some DNA binding
property due to its triphenylphosphonium group. I would like to assess this
using Pymol. How could I do this? I do not have much
Hi, Thomas. Yeah, solution no. 1 worked! Thank you very much indeed.
Kind regards,
Antonio
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Hi Dan and Thomas,
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Perhaps this will do the trick,
Show the protein as surface and cartoon then set the surface to almost
invisible:
set transparency, 0.99
Then set the surface transparency to be angle
Hi Dan,
I think in PyMOL you can only do this in two steps and compose the two images,
e.g. with ImageMagick.
# white background
bg white
# step 1
as surface
set ray_trace_mode, 2
png surface.png, ray=1
# step 2
hide surface
show cartoon
set cartoon_cylindrical_helices
set ray_trace_mode, 1
Hi Stéphane,
Pedro is correct, you should change the selection like he suggested.
You also need to:
- Make a state specific selection with cmd.select(..., state=i)
- Adjust the loop to start at 1 and not at 0
- Use "stored.resid.append(resv)" as the expression
This should work:
###
from pymol
