[Chimera-users] precise overlay of ligands

Tue Jan 13 11:31:03 PST 2009

Hi Elaine,

Thanks so much for all the advice. I'm still having trouble getting  
the match/alignment command to work and I'm not quite sure what I'm  
doing wrong but I think it's in my pdb format. I have attached two  
files with four atoms in each that I would like to overlay and get the  
rms deviation for. Maybe you could look at the files and let me know  
where my formatting mistake is. The files are attached and the  
coordinates are listed below. They both open in Chimera and work fine  
but I think maybe the problem lies in chain id #'s or something.

Thanks again for your help,
Dave

1st pdb file: 2to1_coordinates_test.pdb

HETATM  114  B2  CE2    22       8.649  -5.055  13.615  1.00   
1.00           B
HETATM  115  B3  CE2    22      10.976  -7.450   8.675  1.00   
1.00           B
HETATM  117  S1  CE3    22       8.845  -8.275  11.641  1.00   
1.00           S
HETATM  118  S2  CE3    22      10.227  -5.377  10.923  1.00   
1.00           S
END

2nd pdb file: Cycle_coordinates_test.pdb

HETATM   96  B2  CE2 Z   1      -3.480  14.686 -11.018  1.00   
1.00           B
HETATM   97  B3  CE2 Z   1      -5.877  19.992  -9.560  1.00   
1.00           B
HETATM   99  S1  CE3 G   1      -6.701  16.412 -10.234  1.00   
1.00           S
HETATM  107  S9  CE3 G   1      -3.731  17.766 -10.322  1.00   
1.00           S
END

On Jan 12, 2009, at 6:35 PM, Elaine Meng wrote:

> Hi Dave,
> Me again - I forgot to mention that there is also a command to  
> measure RMSD between sets of atoms without fitting them (it just  
> uses their current positions):
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>
>
> You could fit on the three pairs of atoms using the "match" command,  
> then use this "rmsd" command to measure RMSD between other sets of  
> atoms without changing the fit. I wasn't sure from your mail whether  
> that was something you wanted to do.
> Best,
> Elaine
>
> On Jan 12, 2009, at 1:33 PM, Elaine Meng wrote:
>
>> Hi Dave,
>> With the "match" command you can specify the exact atoms to fit, and
>> the resulting RMSD will be reported in the Reply Log. The main thing
>> to be careful about is specifying the atoms in the proper order.  One
>> way is by name, another is to pick them in order from the graphics
>> window (Shift-Ctrl-click).
>>
>> Specifics on how to use the "match" command:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
>>
>> More general information on various matching methods:
>> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>                     http://www.cgl.ucsf.edu/home/meng/index.html
>>
>>
>> On Jan 12, 2009, at 1:32 PM, David Chenoweth wrote:
>>
>>> Dear Chimera team,
>>>
>>> Hi! I have two ligands in two different PDB files which have a very
>>> similar core structure. I have constructed a framework of dummy
>>> atoms based on the centroids of several aromatic rings to use as a
>>> positioning system for the two ligands. I have three points/dummy
>>> atoms for each ligand in space in their respective pdb files and I
>>> would like to overlay or map the three points of one onto the three
>>> points of the other so I can make measurements in chimera. Is there
>>> a simple way to open the two pdb files, select the three points that
>>> belong to each ligand and overlay them (maybe even minimize the rms
>>> deviation between them with some kind of fit to the plane defined by
>>> the three points). I can do this by hand and get them close but not
>>> exact. I would also like to be able to calculate the rms deviation
>>> between similar atoms in the core structure if possible.
>>>
>>> Thanks in advance,
>>> Dave Chenoweth
>

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