[Chimera-users] superimpose --matchmaker.

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 19 09:57:02 PST 2007

Hi Vinay,
The important thing for matchmaker is not the input format, but the  
type of structure: peptide/protein or nucleic acid chains are  
handled.  These could be read from PDB, mmCIF, or Mol2 formats if  
described as chains of amino acid or nucleic acid residues (i.e. not  
one giant residue).

For "match," it also does not matter much what input format you use.   
Once the structure is read in, it is treated basically the same way.   
It is better if the atoms have unique names, however (e.g. C1 C2  
C3 ... instead of all "C"), since then you can use the atom names  
with the "match" command.  The most commonly used formats (PDB, Mol2,  
CIF/mmCIF, MDL MOL/SDF) all accommodate unique atom names.

Even if the structures don't have unique atom names, it may be  
possible to specify the atoms for the "match" command in some other  
way, such as by picking them from the graphics window.  If you  
specify by picking (Ctrl-left button click by default), be careful to  
pick the atoms in the correct order, as described in the "match" man  

Finally, sometimes you can get away with just using the residue name  
(e.g. "match #1:fad #0:fad"), but usually that will not work well  
because the atoms are in a different order, or even if they are in  
identical order and chemical correspondence, the names could be  
reversed from what would give the best match in space.  A simple  
example is two Asp residues, where you might get a better RMSD by  
matching OD1/OD2 and OD2/OD1 instead of OD1/OD1 and OD2/OD2.  OD1 and  
OD2 are chemically indistinguishable but named differently.

That may have been more detail than you wanted.  8-)
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 18, 2007, at 11:51 PM, Vinay Kumar wrote:

> Hi all,
> There have been a few posts previously regarding superimposing of
> molecules. using matchmaker would work for a pdb file. I was curious
> if small molecules (ligands) could be matched. I did check out the
> documentation and the command match. But what i am not sure abt is, in
> wht format should the input file for a small molecule be??
> could someone suggest!!
> regards,
> Vinay

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