From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Nov 24 2016 - 22:41:36 CST

Hi,

There are multiple approaches one can take.

E.g. If two proteins are roughly the same size you could make 2 selections
on structures. 1 comprising of 1st and the last residues CA only of protein
1 and the same for protein two. Now you can use measure fit to get a
transformation matrix between the two selections. This would do a rough
global alignment.

Another approach could be from one of the previous answers. You don't need
to have Sam number of lysines. You can choose say 5 from structure 1 in
selection 1 and 5 from structure 2 in selection 2.

Yet another approach could be that You could use external programs like
gesamt , superpose, fatcat etc to superpose the two structures which don't
need structures to be equal. They would return a structural alignment. They
would also return a transformation matrix which you could import into vmd
and use to see how your superposition looks by applying it on the query
structure to map onto the target.

Let me know if you need more detail.

Hope this helps.
Best,
/A

On Nov 25, 2016 16:07, "Wong Li Zhe" <Wong.LiZhe_at_student.imu.edu.my> wrote:

> Dear all,
>
>
> Thanks for all the valuable suggestion.
>
> STAMP won't work for my case as my residues are in thousands and it
> literally freeze when I tried to run it.
>
> I did tried looking for homologous section but I couldn't.
>
> For instance, there are total of 9 LYS in protein A but not the case in
> protein B. It either appears to have more than 9 or less than 9.
>
> And I don't think deleting/adding the residues is the right move.
>
> Any suggestions or did I misunderstood any of the suggestions here?
>
>
> Thanks!
>
>
> Best regards,
>
> Li Zhe
> ------------------------------
> *From:* John Stone <johns_at_ks.uiuc.edu>
> *Sent:* Friday, 25 November, 2016 2:16:21 AM
> *To:* Vermaas, Joshua
> *Cc:* Wong Li Zhe; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Superimpose Models
>
> 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
> >
> >
> > [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.
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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
> >
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>
> [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
>
>
>
>
> 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
>
>