Hi Jason,
Coming back to an older thread:
On Thu, Aug 19, 2010 at 10:57 PM, Jason Vertrees
wrote:
>
> I moved the 0.99 build download page because I didn't have a good
> place for it during the reorganization. I'll add them back when I
> update the Download page.
>
Since I remembered this mess
Hi Thomas,
PyMOL can detect cavities and voids on its own. From the upper
control window, select
Settings > Surface > Cavities and Pockets
and then show your object or selection as surface, which will show the
cavities as surface, not the outer molecular surface.
If you need a properly vetted
I find HOLLOW (http://hollow.sourceforge.net/) to be quite good.
On Fri, Dec 3, 2010 at 12:15 PM, Thomas Evangelidis wrote:
> Dear Pymol users,
>
> I want to display clearly the volume of a buried cavity inside my protein.
> Does anybody know how to do this? I've tried CastP and Caver plugins
> a
Hi, Tom,
have a look at MSPocket:
http://appserver.biotec.tu-dresden.de/MSPocket/
It uses MSMS to generate protein solvent excluded surface (SES) and then
detects pockets on the SES. It also calculates the volume for cavities
(internal pockets buried in proteins) based on the SES.
cheers,
hongbo
Dear Pymol users,
I want to display clearly the volume of a buried cavity inside my protein.
Does anybody know how to do this? I've tried CastP and Caver plugins
already, but they do not produce exactly the volume I want to display. I
would greatly appreciate any advice.
thanks,
Tom
-
Hi Björn,
The command you're issuing,
> cmd.pseudoatom('grid', pos=[i,j,k], color='white')
is asking PyMOL to create an object called 'grid' -- which on
subsequent calls will just append the pseudoatoms to original 'grid'
object created from the first call. If you want, say 10, individual
objec
Hi,
I would like to generate a bounding box (grid) of pseudoatoms.
I do this by the following command:
cmd.pseudoatom('grid', pos=[i,j,k], color='white')
My problem is, that from step to step, the algorithm slow down. I
think that in each step pymol build up a new object. But he should
only
