[Chimera-users] holle,sir!

[Elaine Meng]

On Jan 29, 2010, at 10:14 PM, gytjyb wrote:

> holle,sir! nice to send a letter to you!
> (1) about FindHBond .I can find out some HBond between ligand and  
> receptor,by chimera. I also use Accelrys Discovery Studio to find  
> out some HBond . but Accelrys Discovery Studio find out HBond to be  
> more than chimera.  why?which one result is ture?
> (2)what is meaning about Clashes/Contacts?what is useful for Finding  
> Clashes/Contacts
> (3)how can i find out interaction between ligand and receptor and  
> classify displaying.
> (4)can i use this software to publicate my paper ,directly?
> best wishes for you !

(1) FindHBond vs. other programs.
Different programs use different methods and cutoffs, and there is no  
reason to expect exactly the same results.  The world of science does  
not agree on one exact definition of H-bond.  Each program should  
explain its own method, as we have in the FindHBond documentation.   
Click "Help" on the FindHBond dialog or go here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html 
 >

Also, this same question was discussed 2 days ago on the chimera-users  
list, see:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-January/004746.html 
 >

(2) What are clashes and contacts?
This is explained in the Find Clashes/Contacts documentation. Click  
"Help" on the Find Clashes/Contacts dialog or go here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
 >

(3) use FindHBond and Find Clashes/Contacts. The "Structure Analysis  
and Comparison" tutorial is one example of using these tools:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
squalene.html>

(4) yes, you can use images and calculation results from Chimera in  
your paper, but please remember to credit Chimera as described here:
<http://www.cgl.ucsf.edu/chimera/docs/credits.html>

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco