VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 15 2005 - 11:19:43 CDT

Hi,
  Sorry for the delayed reply, but I've been out of town for the last
week. I do try to keep up, but you guys need to give me more
than 24 hours to respond to emails when I'm out of town :-)

In general option A) is the best approach. So long as you use "waitfor all"
there shouldn't be any performance difference between the various choices,
but A) is the way things are done now, and the other options may be officially
outdated or removed at some point in time, so I do recommend people start using
the 'mol new' and 'mol addfile' way of doing things. And, regarding the
use of 'animate read' with a selection, that is only intended to be used with
writing, as you've discovered it's not valid to use on reads.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 14, 2005 at 09:19:33PM +0800, Jian Zou wrote:
> Hi all,
>
> I have some questions about the usage of mol, animate.
>
> first:
> Is there some difference between the following 3 sets of commands?
> Which should be more efficient or recommended to use for loading structure &
> trajectory files?
> A.
> mol new alanin.pdb
> mol addfile alanin.dcd waitfor all molid top
> B.
> mol new
> animate read pdb alanin.pdb top
> animate read dcd alanin.dcd waitfor all top
> C.
> mol load pdb alanin.pdb dcd alanin.dcd
>
> second:
> animate [read|write] <file type> <filename>
> [|beg <num>] [|end <num>] [|skip <num>] [|waitfor <num/all>]
> [|sel <atom selection>] [|<molecule id>]
> I tried "animate read ..." with some selection but failed.
> Can anyone show me an example on how to "read" with "selection"?
>
> Thanks a lot in advance.
>
>
> Regards,
>
> Jian Zou 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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