[Chimera-users] Molecular representation & FindHbond

[George Tzotzos]

Apologies. I did not attach the snapshot. I do so now

Many thanks

George


-------------- next part --------------
A non-text attachment was scrubbed...
Name: snapshot.tiff
Type: image/tiff
Size: 91636 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20110530/baa63dc0/attachment.tiff>
-------------- next part --------------




On May 30, 2011, at 8:25 PM, George Tzotzos wrote:

> Hi everybody,
> 
> I've successfully loaded my protein. It is represented in ribbon.
> 
> I want to select three specific residues (e.g. HIS22, TYR53 and VAL124), show them in ball & stick and find Hbonds between them.
> 
> I follow the procedure below:
> 
> 1. select #0:22,53,124. Chimera returns: 55 atoms, 54 bonds
> 
> 2. show sel
> 
> 3. repr bs sel
> 
> 4. FindHbond (see snapshot). Nothing is displayed. Instead, I see under the command window: 109 hydrogen bonds found. These are ALL the Hbonds found in the protein.
> 
> I'd appreciate your guidance how to deal with this.
> 
> Another related issue is the carboxy terminal residue. In this case VAL124. It is deprotonated. Is it possible to protonate it and then look for Hbons?
> 
> Thanks in advance for your advice
> 
> Regards
> 
> George
> 
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users