VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 16 2015 - 01:52:34 CST

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