VMD-L Mailing List

From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Thu Jan 14 2016 - 05:37:52 CST

Hi,
I intend to load max 30 volumes or a number of users choice.
Currently I use a workaround which loads for every eight volumes a new
molecule.
Or to say it better: after 8 times pmepot for a new frame, I load the
molecule as a new one and go on with pmepot for the next frames.
After this I read with interpolvol the potential around the atome(s) of
interest, calculate the coloumb energy and write this to a file.

Do you need the script as an example?

Sincerely

Daniel Möller

-----Ursprüngliche Nachricht-----
Von: John Stone [mailto:johns_at_ks.uiuc.edu]
Gesendet: Mittwoch, 13. Januar 2016 20:38
An: Daniel Möller
Cc: VMD Mailing List
Betreff: Re: vmd-l: question about reading more volumes via atomselect or
removing of them

Hi,
  At present, the implementation of the 'volN' and 'interpvolN'
selection keywords is based on hard-coded strings because the atom selection
language doesn't implement the concept of array indices for the volumetric
data yet. It is easy to extend the number of volumes that can be selected
by something on the order of 2x with trivial changes to the code. If you're
intending to work with a much larger number of volumetric data objects (say
50 or 100), then that might not be very useful, but if you just need
something on the order of 10, that is easy for me to add quickly. Let me
know what you're doing and I'll see if I can give you at least some kind of
short-term solution that's easy to use for the time being.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 13, 2016 at 03:33:13PM +0100, Daniel Möller wrote:
> Hi,
>
>
>
> I have some questions for an analyse purpose with a script:
>
> Is there a way to read more than 8 volumes via atomselect (volN or
> interpolvolN
>
> (http://www.ks.uiuc.edu/Research/vmd/current/ug/node90.html)) from one
> molecule?
>
> I can load more than 8 volumes in a molecule and use them as
> representations, but couldn't read them all.
>
>
>
> If this is not working:
>
> How can I remove volume files from molecules?
>
>
>
> I found some old mails with same questions, and that it's on the TODO:
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8893.html
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12692.html
>
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/13891.html
>
>
>
> Thanks for your help.
>
>
>
> Sincerely
>
>
>
> Daniel Moeller
>
>
>
> --
>
> ------------------------
>
> Dipl. Biochem. Daniel Moeller
>
>
>
> Biophysical Chemistry
>
> Institut of Biochemistry
>
> Unversity of Greifswald
>
> Felix-Hausdorff-Strasse 4
>
> 17489 Greifswald - Germany
>
>
>
> Tel +49 3834 86 4406
>
>
>
>
> http://www.mnf.uni-greifswald.de/institute/institut-fuer-biochemie/bio
> physikalische-chemie.html
>
>
>
> 

--
NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute
for Advanced Science and Technology University of Illinois, 405 N. Mathews
Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/