[Chimera-users] FindHBond

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 14 17:18:09 PST 2009

On Dec 14, 2009, at 4:32 PM, Greg Friedland wrote:

> I'm new to Chimera and just discovered the FindHBond tool. This tool  
> seems very useful, but unfortunately it draws hbonds between the  
> heavy atoms even when I have hydrogens added. Is there a way to  
> configure this behavior? I'd like the hydrogen bonds to be drawn  
> between the hydrogen and the acceptor atom. It looks rather strange  
> now, especially for the hbonds with relaxed constraints that deviate  
> significantly from the angle made by the hydrogen.  See the attached  
> tiff for an example.

Hi Greg,
	There is no capability for that now.  I expect that capability in the  
1.5 release, and will add your name to the Trac ticket for that  
enhancement, so you will automatically get notified when it gets  
implemented.  In the interim, if you execute the attached Python  
script the hbond donor terminus will be moved to the appropriate  
proton.  Execute the script simple by opening it with File...Open or  
with the "open" command.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20091214/d473621e/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: hbondhyd.py
Type: text/x-python-script
Size: 520 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20091214/d473621e/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20091214/d473621e/attachment-0001.html>

More information about the Chimera-users mailing list