[Chimera-users] how to use hbonds spec

Elaine Meng meng at cgl.ucsf.edu
Wed May 7 08:59:36 PDT 2008

Hi Miguel,
The "selRestrict" keyword only works on the selection (what is  
outlined with green).  It sounds like you already figured out that  
the selection must be done in a separate command, since "hbonds"  
doesn't select atoms.  The "spec" keyword can be used to specify a  
particular model but not anything smaller (i.e. not a particular  
residue or set of atoms, only the whole model), and it does not  
select anything.

The remaining issue is how to prevent the selection outline from  
appearing.  In MD Movie, the display is only updated after the per- 
frame script is executed, so you just need to add a command to turn  
off the selection after the hbonds are calculated:

select :100
hbonds selRestrict cross relax false

If this was done in a command script outside of MD Movie, the way to  
suppress intermediate display is to string commands together with  

select :100; hbonds selRestrict cross relax false; ~select

(that should be all one line even if the annoying mail program breaks  
it up!)

It does seem a bit inefficient to keep selecting/deselecting the same  
thing, but that is the only method I can think of currently.   I will  
ask the others about perhaps adding a preference option to suppress  
the selection highlighting.

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 May 7, 2008, at 6:40 AM, Miguel Ortiz-Lombardía wrote:
> I'm trying to follow hydrogen bonds in a trajectory from amber. To  
> do so, I would like to run a 'per frame' script with something like:
> hbonds spec :100 selRestrict cross relax false
> However, this fails because apparently no atoms are selected. This  
> fails as well:
> hbonds spec #0:100 selRestrict cross relax false
> I can only see the hydrogen bonds if insert a
> select :100
> before the hbonds command. I wouldn't like to see the green 'aura'  
> of the selection, that's why I would like to make the selection  
> within the hbonds command. I'm probably missing something, but  
> cannot figure out what.
> Thank you!

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