[Chimera-users] What is exactly matchDist?

[Elaine Meng]

Hello,
Yes exactly, 

 "Each pairwise comparison creates an attribute of the residues of one structure containing the distances from the sequence-aligned residues of a reference structure.” 

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#assessment>

… and you are right that the measurement is between the CA atoms. If a residue is not aligned in the sequence alignment with any residue in the reference structure (i.e. the reference structure has a gap at that position), that particular residue will have no value for the matchDist attribute.

As also described in the link above, you can also calculate RMSDs over all structure residues in a column of the multiple alignment, and these are also assigned as attributes that could be used for coloring or shown in the “worms” representation.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 4, 2018, at 12:10 PM, Murpholino Peligro <murpholinox at gmail.com> wrote:
> 
> Got 8 x-ray structures. Load them into Chimera and did Structure Comparison -> MatchMaker (with multiple sequence alignment). In the alignment I choose Structure-> Asses Match and it creates a residue attribute named matchDist. 
> 
> I guess is the Distance in angstroms for every alpha carbon in my ith structure (where i=1, 2, 3, ...7) to every matching alpha carbon in my reference structure?
> 
> Thanks
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