[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.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>

Elaine

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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