Hello all,
The surface rendering in PyMOL is quite nice, but I cannot separate the
"branches" of the surface. That is, I would like to view a large cavity
inside of a protein independently from the outer, solvent accessible
surface. Is anyone aware of a means to do this?
Marcus Collins
**
Hi Marcus,
> The surface rendering in PyMOL is quite nice, but I cannot separate the
> "branches" of the surface. That is, I would like to view a large cavity
> inside of a protein independently from the outer, solvent accessible
> surface. Is anyone aware of a means to do this?
The easiest way
Have you tried to simply use your mouse wheel? This will change the clipping
view.
Marcus,
Here is one way (courtesy Kyle Lassila):
Check out VOIDOO:
http://xray.bmc.uu.se/usf/voidoo.html
Then:
Use VOIDOO to make a map of the cavity. That gives a
map in one of the electron density formats, .ezd. Then use MAPMAN (also
found as Uppsala Software Factory) to
convert to
Marcus,
Here is one way (courtesy Kyle Lassila):
Check out VOIDOO:
http://xray.bmc.uu.se/usf/voidoo.html
Then:
Use VOIDOO to make a map of the cavity. That gives a
map in one of the electron density formats, .ezd. Then use MAPMAN (also
found as Uppsala Software Factory) to
convert to .ccp
Dear all,
I download CASTpyMOL.pyc and put it in the right folder.
Now I want to use it for detecting cavity for 50 proteins. I don't want
to do that one after one by hand.
Is it possible to write a python (pymol) script to do that automatically?
Thanks a lot!
Regards
Bingding
Sebastie
what about Caver:
http://loschmidt.chemi.muni.cz/caver/concept.php
very nice and it works very well
andrea
2005/11/7, Bingding Huang :
>
> Dear all,
>
> I download CASTpyMOL.pyc and put it in the right folder.
> Now I want to use it for detecting cavity for 50 proteins. I don't want
> to do tha
