[Chimera-users] Molecular representation & FindHbond

George Tzotzos gtzotzos at me.com
Mon May 30 11:25:39 PDT 2011

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



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