Re: vmd-l: Offset for frame ids in dcd trajectory

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 26 2009 - 15:32:40 CDT

Hi,
  There shouldn't be any extra frames, I think both programs
are giving you consistent results. As the frame indexing in VMD
starts at zero rather than one, it ends one sooner as well, but the
total frame count should be exactly the same in both cases. Note that
if you request a frame beyond the end, VMD will likely just return the
last frame, if I recall correctly.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 23, 2009 at 08:11:09PM +0400, DimitryASuplatov wrote:
> Hello,
>
> I have a psf file, and a dcd trajectory.
>
> 1/ If I run
>
> catdcd -num dcd
>
> I have the following output
>
> Read 2140 frames from file 1dwo.md.dcd.
> Total frames: 2140
>
> If I use catdcd to read frames from -first 0 to -last 0 I get null
> output. To my understanding that means that frame numbering starts from
> 1.
>
> 2/ If I run vmd, load psf, then dcd, then run
> set nf [ molinfo top get numframes]
>
> I get
>
> nf=2140, but I cat start selecting frames from 0, that is
> set frame0 [atomselect top "protein and backbone and noh" frame 0] -
> shall work
>
> ==============================================================
>
> Question:
>
> How could you explain an extra frame in dcd trajectory when using vmd?
>
> Thank you for your time.

-- 
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
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

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