VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 12 2012 - 10:34:38 CDT

I would suggest contacting Dr. Oliver Smart, the original author of HOLE
and see if he can send you a copy since the HOLE web site seems to be down
currently:
  http://www.globalphasing.com/people/osmart/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jun 29, 2012 at 02:50:00PM -0400, Raul Araya wrote:
> Dear VMD users
> I want to measure the radius profile of a membrane channel but I have had
> some trouble finding a program that can perform such measurement over a
> namd DCD trajectory. The HOLE program seems to be no longer available to
> download, and the version I have does not work on my Mac, only Linux. I
> have been looking for other programs but most of them require a
> multi-frame pdb file or .dx files with the protein and water density
> (dxtuber), all of which requires some extra time for post-processing the
> trajectories. I will probably use dxtuber but I will like to know if
> anybody have any other solution that can share or a source for the HOLE2
> program.
> Thanks.
> Raul Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Fisicas y Matematicas.
> Universidad de Chile. 

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