VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 12 2011 - 09:13:36 CDT

Hi,
  The "pucker" atom selection query currently returns the Hill-Reilly
pucker value (a single value per ring). I will have to add a new
atom selection query to allow the Cremer-Pople pucker pucker
parameters to be queried within VMD. This will entail building a new
test version of the program, and I probably won't be able to get to it
until next week due to other demands on my time. Bernard, if you can
tell me what platform you are using, I can see about building you a new
test version of VMD that allows the Cremer-Pople pucker paramters to be
queried.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 12, 2011 at 10:03:56AM -0400, Axel Kohlmeyer wrote:
> bernard,
>
> On Tue, Jul 12, 2011 at 8:40 AM, Mr Bernard Ramos <bgrquantum_at_yahoo.com>
> wrote:
>
> Hi Dr. Stone!
> I corresponded with Dr. Michelle Kuttel regarding obtaining Cremer-Pople
> (CP) ring puckering parameters in VMD. Dr. Kuttel gave me your email
> address for this concern.
> I am new to VMD and I am using VMD 1.8.7. I need to have the three CP
> parameters for each frame in my trajectory file. A simple lists for each
> ring in each frame will be fine for me. I hope you can help me with
> this.
>
> you should two three things:
> - upgrade to VMD 1.9
> - familiarize yourself with VMD/Tcl scripting for analysis
> and particularly how to use the atomselect command.
> (there is a special section for that in the user's guide
> and there are tutorials; you may also need to have a
> look at the tcl tutorial at www.tcl.tk).
> - write a suitable analysis script that defines an atom
> selection for your atoms of interest and then use the
> (undocumented?) "pucker" property to retrieve the
> information you desire.
> i strongly suggest to do these things in order and
> don't rush the middle step.
> axel.
>
>
> Thanks,
> Bernard
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA. 

-- 
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