[Chimera-users] Selecting atoms

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 8 08:37:44 PDT 2010

Of course, this presupposes your PDB file actually has hydrogens.  If it doesn't, you can add them with the AddH tool or the command addh.



On Oct 8, 2010, at 8:31 AM, Elaine Meng wrote:

> 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.  
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