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

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 19 10:45:16 PDT 2014

Dear Jo,
It means that you probably didn't select the atoms in the right order.  I'm surprised the value could be so large, even with that error!  If using the selection method (instead of entering the atom names on the command line), you have to select first the atoms one by one in the first structure, then the atoms one by one in the second structure, in the SAME order as you want them to be paired with the atoms in the first structure.

This is mentioned in the instructions:

If you just can't get the selection method to work, you may need to display atom labels so that you can see the atom names and use the atom names in the command instead of "sel".

On Aug 19, 2014, at 1:20 AM, Jo Sourbron <j.sourbron at gmail.com> wrote:

> 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/
> <20140819 RMSD 3655 Angstrom.png>_______________________________________________
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