[Chimera-users] Selecting atoms

[Elaine Meng]

Hi Peter,
You would need to know what the atoms are named to show only these hydrogens specifically.  You could figure out atom names by 

(a) simply showing all atoms ("Actions... Atoms/Bonds... show" in menu or command: display) and hovering the cursor over the atom of interest, which would pop up a balloon with information including the atom name.  Of course, you would then probably want to hide (command: ~disp) all or some of the atoms and then possibly re-display just the ones you want.
(b) looking in the PDB file with a text-editor
(c) knowing the standard PDB name for this atom, assuming your file obeys that system

The PDB standard name for the "para" carbon in a Phe sidechain is CZ, and I believe the name for the attached hydrogen would be HZ, so you'd want something like:

display :phe at hz

Colon means residue, so you want that right before phe, "at symbol" means atom, so you want that before the atom name. I don't know what the "da" was in your example.

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

On Oct 8, 2010, at 6:52 AM, Peter Baker wrote:

> Good Morning. 
>  I am trying to display the H atoms in the para-position of the all the Phe residues. Could anyone offer me some advice on specific key commands which would help me out. I have tried da: phe@ cz but I was not successful . 
> Thanks
> Peter.