VMD-L Mailing List

From: Sourav Ray (souravray90_at_gmail.com)
Date: Mon Feb 16 2015 - 04:36:17 CST

It doesn't work, I substituted "protein" instead of "resid 1 to 10", it
failed to recognize the selection in both the cases.

On Mon, Feb 16, 2015 at 1:22 PM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> animate write pdb myframes.pdb beg 0 end [molinfo top get numframes] sel
> "resid 1 to 10"
>
>
>
> Norman Geist.
>
> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
> Behalf Of *Sourav Ray
> *Sent:* Monday, February 16, 2015 7:32 AM
> *To:* Maxim Belkin
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Extracting coordinates from DCD file to a single
> PDB file
>
>
>
> .psf file for defining the topology and .dcd file for the coordinates. it
> would be convenient to get all the frames in a single pdb file as
> processing will be much easier.
>
> regards
>
> Sourav
>
>
>
> On Mon, Feb 16, 2015 at 11:21 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu>
> wrote:
>
> What do you have as input (file format and content)?
>
>
>
> On Feb 15, 2015, at 23:21, Sourav Ray <souravray90_at_gmail.com> wrote:
>
>
>
> 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
>
>
>
>
>
>
>