VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Sun Feb 15 2015 - 23:21:59 CST

I guess there is some misunderstanding, I would like all the frames in a
single .pdb file, that too sequentially (frame 1, frame 2...). Is it
possible somehow?

On Fri, Feb 13, 2015 at 5:03 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> set nf [molinfo top get numframes]
> set sel [atomselect top "protein"]
> for {set i 0} {$i < $nf} {incr i} {
> $sel frame $i
> $sel writepdb "protein-$i.pdb"
> }
> $sel delete
> mol delete top
>
> If there are multiple proteins use more specific selection text, e.g. use
> resids or something else.
>
> Maxim
>
> > On Feb 13, 2015, at 04:09, Sourav Ray <souravray90_at_gmail.com> wrote:
> >
> > Hello
> >
> > I have been trying to extract all the frames of a protein into a single
> PDB file. There is a code available currently in a thread here for
> extracting each frame in different PDB files:
> >
> > set nf [molinfo top get numframes]
> >
> > for { set i 0 } {$i < $nf } { incr i } {
> > set sel [atomselect top protein frame $i]
> > $sel writepdb $i.pdb
> > }
> >
> > Can someone please suggest a modification that works? Also, what if
> there are multiple proteins? Can we extract each one separately?
> >
> > Regards
> > Sourav
>
>