VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Aug 03 2015 - 13:09:50 CDT

Hi Ben,

How about:

set sel [atomselect top protein]
set pos [measure avpos $sel]
$sel set {x y z} $pos ; #Moves the selected atoms to the average positions computed in the previous step
$sel writepdb avpos.pdb

VMD knows how to write out loaded structures, so what this will do is
reposition all the selected atoms to the measured positions, and then
you write them out to a file.

-Josh Vermaas

On 08/03/2015 12:24 PM, Kuiper, Ben wrote:
> Hi,
>
>
> I am trying to create a single .pdb file of my protein containing the average coordinates over the trajectory. After loading the frames and RMS aligning, I am able to calculate the average position using the following:
>
>
> set sel [atomselect top protein]
>
> measure avpos $sel
>
>
> Once this is completed, I have no idea how to export this as a .pdb file. I have read some of the discussions regarding similar situations (like adapting the trajectory_smooth script) but am not sure how to perform the commands - I am a beginner!
>
>
> Any help would be appreciated,
>
>
> Ben
>
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