Hi James,
the "within" selection operator might solve your problem.
http://pymolwiki.org/index.php/Selection_Algebra#Comparison_of_distance_operators
Hope that helps.
Cheers,
Thomas
On 08 Nov 2014, at 02:26, James Starlight wrote:
> Dear PyMol users!
>
> I'm writing of some automatic script aimed on the embedding of the receptors
> into the membrane consisted of the pre-equilibrated lipids as well as hole
> for the protein. The main issue that some of the receptors consist of the
> bulky PHE or TRP side chains on their surface which are overlap with the
> lipids so MD simulation of this system is crushed although of long
> minimization stage prior to it. I'll be very thankful if someone provide me
> with some script for PyMol or VMD for automatic detection of these problem
> (overlapped) locations and removing of the overlapped lipids detected within
> some cutoff radios of the protein.
>
> Thanks for help,
>
> James
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
--
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