[Chimera-users] [chimera-dev] Protein to ligand shortest distances?

Elaine Meng meng at cgl.ucsf.edu
Mon May 21 10:39:50 PDT 2007

Hi Kate,
The Find Clashes/Contacts tool will report all atoms near your ligand  
and the corresponding distances.  However, it does not work with a  
single strict cutoff, but instead uses the atoms' VDW radii.  For  
example, if you used a cutoff of 0.0 overlap, that would find all  
atoms with VDW surfaces either intersecting or just touching.  It  
finds all the atoms meeting your specified cutoff criteria, so you  
would still need to look at the list of results to see which atom is  
the closest from each residue.  There are two cutoff parameters, the  
amount of VDW overlap and the extra closeness allowed for H-bonding  
pairs.  As mentioned in the manual page,


the suggested values for these two parameters are:
  0.4-1.0 and 0.2-0.6, respectively, if you only want to detect  
"clashes" (unfavorably close contacts)
  -0.4-1.0 (negative values) and 0.0, respectively, to detect  
contacts in general

It sounds like you want the latter.  Select your ligand (for example  
by Ctrl-click on one atom and then hitting the keyboard up arrow),  
open the tool (Tools... Structure Analysis... Find Clashes/Contacts),  
click "Designate" to specify you want to find contacts of the  
selected atoms (the ligand) versus all other atoms.  Set the  
parameters to -0.5 and 0.0.  In the bottom section check "Write  
information to reply log" and uncheck the other options.  Open the  
reply log (it's in the Favorites menu).  Click Apply and the list of  
results will be written in the Reply Log window.  You could play  
around with the VDW overlap parameter and when you think you have  
what you want, you could use the "Write information to file" instead  
of the reply log.  As I mentioned above, you would still have to look  
through the results to see the closest atom from each residue.  The  
more negative the parameter, the more atoms will be found (including  
those which are further away from the ligand).  There is also a  
command version of this tool,

If you really care that you include all residues with any atom within  
5 angstroms, you could do an additional step first:  select the  
ligand, then Select... Zone using 5 angstroms, then use Actions...  
Write List to save the names of the "selected residues" to a file.   
You can compare this list to the more detailed results from Find  
Clashes/Contacts to find the closest atom from each of the residues.

I hope this helps,

p.s. I'm sending this to chimera-users too because that is more for  
user questions, while chimera-dev is more for developer/programmer  
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 May 20, 2007, at 10:12 PM, khar6039 at mail.usyd.edu.au wrote:

> Hi all,
> I'm new to chimera and would like a simple way to zone 5 Angstroms  
> around a
> ligand and then have chimera tell me what the shortest distances are
> between these residues and the ligand. Is this possible?
> Cheers,
> Kate

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