[Chimera-users] Match two small molecules with command line : "match"

Jo Sourbron j.sourbron at gmail.com
Tue Aug 19 01:20:56 PDT 2014


Dear,

thank you very much for this reply.
I tried is with the Shift-ctrl-click, then selecting the 2 structures at
once. Then I gave the command: match sel , and then the program calculated
a RMSD = 3665 Angstroms. But what does this mean exactly? Is there anyway I
can let the program overlap this 2 structures?


Looking forward to your answer,
Kind regards,
Jo Sourbron


2014-08-12 19:48 GMT+02:00 Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Jo,
> For small molecules, you have to tell Chimera which atom to match with
> which atom; it doesn't figure it out automatically.  If the molecules were
> the same chemical and had exactly the same atom names, your command could
> be something like:
>
> match #1 #0
>
> … which would keep your first structure (model #0, with tan carbons) in
> place and fit the second structure (model #1, with light blue carbons) onto
> it by pairing all atoms with all atoms based on their names.  If you only
> give model number and no residue or atom names, it means all atoms.
>
> However, these two are not exactly the same compound, so instead you have
> to give all the names of the atoms in the same orders that you would like
> them to be paired, or use Shift-ctrl-click to pick them in the same order
> and then use "sel" in the command as the atom-spec.   Here is an example of
> using atom names, but of course you would have to use the names that are
> really in your molecules (could use command "label" to show them):
>
> match #1 at c1,c2,c3,c4,o1  #0 at c6,c1,c2,c3,n1
>
> … which would pair C1 in model #1 with C6 in model #0, C2  in #1 with C1
> in #0, etc.
>
> There are more examples and explanation in the "match" manual page:
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>
> Specifying the atoms by name is only one way.  There are many other ways,
> as explained in the "atom spec" manual page:
>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> >
>
> 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 Aug 8, 2014, at 4:30 AM, Jo Sourbron <j.sourbron at gmail.com> wrote:
>
> > Dear,
> > I really appreciate the features that Chimera has (as I read them in yhe
> user's guide).
> > Though there seem to be a problem:
> > I want to match two small molecules (and in the future maybe more), but
> If I open the pdb files in Chimera and use the command line match, it says
> that there is missing an atom spec.
> > Then I looked again in the user's guide and I noticed the "#" that they
> use.
> >
> > I don't know how what this "#" means. I just want to overlap the two
> structures and get a percentage of homology or something like that. That
> would be great.
> >
> > You can always contact me,
> > kind regards,
> > Jo Sourbron
> > PhD Student
> > Laboratory for Molecular Biodiscovery
> > Department of Pharmaceutical and Pharmacological Sciences
> > Katholieke Universiteit Leuven
> > O&N2, Campus Gasthuisberg
> > Herestraat 49, box 824
> > B-3000 Leuven, Belgium
> >
> > j.sourbron at gmail.com
> > GSM.   +32 474 94 84 17
> > TEL.     +32 16 37 78 07
> > http://be.linkedin.com/pub/jo-sourbron/33/496/77a/
>
>
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