VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Nov 24 2016 - 11:27:49 CST

Hi Li,

The normal way of doing this would be to make sure two selections from each protein have the same size, not two pdbs. Perhaps residues 1 to 24 of protein A are homologous to residues 35 to 58 of protein B, then you could make a selection like this to align the two proteins based on those homologous sections:

mol new proteinA.pdb
set ref [atomselect top “name CA and resid 1 to 24”]
mol new proteinB.pdb
set all [atomselect top “all”]
set sel [atomselect top “name CA and resid 35 to 58”]
$all move [measure fit $sel $ref]

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Nov 23, 2016, at 11:40 PM, Wong Li Zhe <Wong.LiZhe_at_student.imu.edu.my<mailto:Wong.LiZhe_at_student.imu.edu.my>> wrote:

Dear VMD users,

I would like to combine superimpose 2 protein models with different atoms numbers.
I wonder is there a way in which how I can alter the PDB file to achieve the same atom numbers?
I have tried several approaches using Tk console and etc but it wont.
Any insight on this issue?

Thank you.

Best regards,
Li Zhe

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[http://www.imu.edu.my/e-banner/fisday-3Dec.jpg]
An opportunity to learn about our Foundation in Science (FiS) programme.
Join many exciting activities for the day.
Start your future in healthcare at our FiS Info Day!
More at http://ask.imu.edu.my/foundation

[http://www.imu.edu.my/e-banner/fisday-3Dec.jpg]
An opportunity to learn about our Foundation in Science (FiS) programme.
Join many exciting activities for the day.
Start your future in healthcare at our FiS Info Day!
More at http://ask.imu.edu.my/foundation