From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 24 2016 - 12:16:21 CST

Hi,
  I would also add that if one doesn't know which residues are
homologous, you should be able to use the alignment tool
(based on STAMP) in the Multiseq plugin to do both the homologous
residue determination and the structure alignment automatically.
That approach is pretty effective if one only needs to align two or
a relatively small number of structures (e.g. not thousands).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 24, 2016 at 05:27:49PM +0000, Vermaas, Joshua wrote:
> 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
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-- 
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