VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Feb 17 2015 - 01:57:28 CST

You need to use the correct molecule id for the atomselection, if the
molecule isn't top. You find the id in the VMD Main window on the left.

 

set molid 1

set a [atomselect $molid "resid 1 to 10"]

 

If the molecule has frames, than this should output the correct number:

 

molinfo $molid get numframes

 

So this command should output all the frames then:

 

animate write pdb myframes.pdb beg 0 end [molinfo $molid get numframes] sel
$a

 

Norman Geist.

 

From: Sourav Ray [mailto:souravray90_at_gmail.com]
Sent: Tuesday, February 17, 2015 8:20 AM
To: Norman Geist
Cc: VMD Mailing List
Subject: Re: vmd-l: Extracting coordinates from DCD file to a single PDB
file

 

Hello

It writes one frame only. Can you please suggest some modification?

Regards

Sourav

 

On Mon, Feb 16, 2015 at 6:03 PM, Norman Geist
<norman.geist_at_uni-greifswald.de> wrote:

>From the help it wasn't clear, but you need to do:

 

set a [atomselect top "resid 1 to 10"]

animate write pdb myframes.pdb beg 0 end [molinfo top get numframes] sel $a

 

Norman Geist.

 

From: Sourav Ray [mailto:souravray90_at_gmail.com]
Sent: Monday, February 16, 2015 11:53 AM
To: Maxim Belkin
Cc: Norman Geist; VMD Mailing List

Subject: Re: vmd-l: Extracting coordinates from DCD file to a single PDB
file

 

Hi Maxim

I got 1 2 .. 12 13 after executing the last line.

Regards

Sourav

 

On Mon, Feb 16, 2015 at 4:13 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

Can you share with us the result of the following two commands?

 

set sel [atomselect top "protein"]

puts "[lsort -unique -integer [$sel get resid]]"

 

 

On Feb 16, 2015, at 04:36, Sourav Ray <souravray90_at_gmail.com> wrote:

 

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