VMD-L Mailing List

From: Kuiper, Ben (bkuiper_at_med.wayne.edu)
Date: Mon Aug 03 2015 - 12:24:08 CDT

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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