VMD-L Mailing List

From: Elijah Roberts (erobert3_at_scs.uiuc.edu)
Date: Tue Oct 07 2008 - 15:13:16 CDT

Hi, you can actually look at the pairwise RMSD (along with QH and PID)
in MultiSeq. After you have aligned them in MultiSeq using STAMP, simply
select both sequences (such as by clicking on one and then ctrl/cmd
clicking on the other) and the pairwise RMSD, PID, and QH values appear
in the status bar of the MultiSeq window.

If you have more than two structures, you can also get all of the
pairwise values by creating a RMSD based phylogenetic tree
(Tools->Phylogenetic Tree) and then looking at the distances using
View->Distance Matrix.

Elijah

John Stone wrote:
> Hi,
> I may be mistaken, but I don't recall MultiSeq having a
> pairwise RMSD using STAMP. It may be possible to implement
> one, but I don't recall that being a built-in feature. I'm
> CCing the main MultiSeq developers in case they wish to
> comment on this further.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Oct 03, 2008 at 08:10:16AM -0700, Dong Xu wrote:
>
>> Hi,
>>
>> How do I calculate pairwise RMSD on a set of PDBs in which the
>> proteins have slight different number of atoms? I aligned them using
>> MultiSeq Stamp structural alignment, but couldn't figure out the
>> pairwise RMSD. I thought it used to be in MultiSeq, but not anymore?
>>
>> Thanks,
>>
>> -DX
>>
>
>