Re: Offset for frame ids in dcd trajectory

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Sat May 23 2009 - 12:15:01 CDT

Hi Dimitry,

 From my understanding these two methods are telling you the same
thing. There are in fact 2140 frames in your dcd. catdcd looks like it
starts its numbering at 1 (in fact it says this specifically in the
documentation), whereas VMD starts at 0. If you try to export frame
2140 with writepdb in VMD, you'll find that that that frame does not
exist. VMD isn't adding anything.

Josh

On May 23, 2009, at 9:11 AM, 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.
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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