[Chimera-users] Measurement similarity protein structure

Nail Besli beslinail at gmail.com
Thu Jul 18 13:02:28 PDT 2019

Hi Elaine.
I am the new user of chimera. I need some help about molecular docking. I
have a ligand and its reseptor. I would like to dock ligand to in certain
residue in the reseptor. I know where I need to do docking which residue. I
need to see a link ligand and residues in the reseptor.

9 Tem 2019 Sal 21:22 tarihinde Elaine Meng <meng at cgl.ucsf.edu> şunu yazdı:

> Hi Nail,
> There is no reason the 3D superposition and RMSD result has to be
> different. The two scoring methods for sequence alignment might give the
> same sequence alignment, or even if the sequence alignment is partially
> different, the iterative 3D fitting starting from the sequence alignment
> might end up using the same positions of the proteins in the final fit.
> If you use the option to show sequence alignment, it will show the
> sequence alignment and draw light orange boxes on the alignment indicating
> the positions of the 3D structures used in the final fit.
> For more explanation of how Matchmaker works, see the manual page.  There
> is also a publication, if you really want to read even more.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html
> >
> 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 9, 2019, at 2:21 AM, Nail Besli <beslinail at gmail.com> wrote:
> >
> > Hi
> > I superimposed two proteins in chimera with winch algorithms( blossom62)
> and p250. The result is the same. Why is the result same for both two
> proteins, although I tried two different algorithm settings? I  am using
> the chimera's MatchMaker tool. The only thing different is the sequence
> alignment score. I attached the result file.
> > kind regards
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