[Chimera-users] Structure superimposition - RMSD

[Suda Parimala Ravindran]

Thanks, Elaine! Would try up and let you know if I get onto more
queries..!! :-)

Best,

Suda

**







On Thu, Nov 17, 2011 at 8:44 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Suda,
> From the Reply Log it looks like the Match->Align calculation did not run:
>
> Match?Align cutoff: 5.0, in column if within cutoff of: any
> Cannot generate alignment with Bitis gabonica.pdb principal chain because
> it is not superimposed on the other structures
> Match?Align cutoff: 5.0, in column if within cutoff of: any
> Cannot generate alignment with Bitis gabonica.pdb principal chain because
> it is not superimposed on the other structures
>
> ... and this would suggest no sequence alignment including all 10 (or 5?)
> was output, or even if something was output, the calculation did not
> finish.  I only see pairwise RMSD results from MatchMaker.
>
> I think your approach to try each possible reference is reasonable.
>  Another possibility is to try to find one that generally has smaller
> pairwise RMSDs with the others, but that can be difficult, so what you were
> doing sounds fine.
>
> However, be careful to pick the chains in the Match->Align dialog that are
> superimposed.  You can "clear" the Reply Log before running Match->Align so
> that you will not be confused by the results from MatchMaker.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
> On Nov 16, 2011, at 10:15 PM, Suda Parimala Ravindran wrote:
>
> >
> > Hi Elaine..
> >
> > Thanks a lot for your reply. I have run even the Match-> Align along
> with iteration. After running, the alignment window does show up, I have
> checked the reply log. But can't find the overall RMSD value for some runs.
> I have attached the entire reply log file along for which i didn't find the
> overall value. So can you please help me locate the overall RMSD value? I
> can only find the pairwise RMSD values.
> >
> > Also, I want to know on how to choose a reference structure. Say for
> example, i have 10 structures to superimpose and among them 5 belong to
> (eg) bacterial species (my query/study of interest) and the remaining 5
> belong to varied organisms of different hierarchy. So how do i choose my
> reference structure among the 5 from my query. what I thought was to run
> the superimposition 5 times choosing each bacterial strcuture as a
> reference each time, calculate the overall RMSD and then choose the least
> RMSD one as reference? Can i proceed this way or are there any other better
> option to choose a reference structure?
> >
> > PLease help.
> >
> > Thanks,
> >
> > -Suda
> >
> >
> >
> >
> >
> >
> >
> >
> > On Wed, Nov 16, 2011 at 11:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> > Hi Suda,
> > Matchmaker does pairwise superpositions to the reference, so even if you
> chose to match structures B,C,D to A, it will perform pairwise matches and
> report pairwise RMSD for A-B, A-C, and A-D.  All of those should be in the
> Reply Log, but there is various other stuff between them such as parameters
> listings, so you would need to scroll up to see them.
> >
> > However, to get an overall RMSD of more than two structures, after you
> run MatchMaker you would run Match->Align to make a multiple sequence
> alignment (instead of the pairwise ones created by MatchMaker).
>  Match->Align is in the menu under Tools... Structure Comparison.
> > <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchalign.html
> >
> >
> > Besides overall RMSD it will also give you other measures of structural
> similarity (SDM, Q-score), and in the output sequence alignment there will
> be an RMSD histogram above sequences showing the per-column values.
> >
> > HOWEVER, be aware it will take a pretty long time to run Match->Align on
> 10 structures, especially with iteration.  I would try it without iteration
> first (which still might take a pretty long time, many minutes) and see if
> the resulting sequence alignment looks good enough.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > On Nov 15, 2011, at 8:31 PM, Suda Parimala Ravindran wrote:
> >
> > > Hi all,
> > >
> > > I have a set of protein structures (about 10) that I need to
> superimpose. I have used Matchmaker and superimposed by choosing a
> reference structure. I want to know how to calculate the overall RMSD of
> the superimposed structures? Where do I lokk out for it? I have checked the
> Reply log window, but it gets displayed only for some, whereas for others
> it does not. Please help..
> > >
> > > Thanks,
> > >
> > > -Suda
> >
> >
> > <Reply_log.txt>_______________________________________________
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>
>
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