Re: extracting avarage pdb from dcd file

From: Souvik Sinha (
Date: Mon Sep 11 2017 - 10:19:51 CDT

I think this may work

set sel [atomselect top all]
set avg [measure avpos $sel]
$sel frame 0
$sel lmoveto $avg
$sel writepdb avg.pdb

On Mon, Sep 11, 2017 at 11:18 AM, Srijita Paul <> wrote:

> Hi,
> I am trying to creat a avarage pdb file from my dcd file to get a avarage
> structure of my system.For that I am using the following script
> set sel [atomselect top all]
> set avg [measure avpos $sel]
> set coords [$sel get {x y z}]
> set {x y z} $avg $sel
> writepdb avgpdb.pdb $sel
> set {x y z} $coords $sel delete
> After running it in tk console the following error is coming-
> wrong #args : should be "set VarName ? New Value ?"
> Please give me a way out or provide me a script to get avarage pdb from
> dcd.
> thank you

Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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