[Chimera-users] Selecting atoms

Forbes J. Burkowski fjburkow at plg.uwaterloo.ca
Thu Oct 28 07:13:32 PDT 2010

We are trying to assess relative strength of hydrogen bonds using a
formula such as that on page 1336 of the paper by Dahiyat et al. (Protein
Science, 1997 (6) 1333-1337).  This formula takes angle information into
account, but it requires the position of the hydrogen atom.  My question
is: If I use AddH, do I get a position of the H atom that is reliable
enough to allow us to use this formula?

It occurs to me that AddH might be computing a position that would
minimize the value of the energy function specified on page 1336, but I am
not sure if this is the case.

Can you give us any advice on these issues?  Is there another formulation
that I could use with Chimera?

Best regards,
Forbes Burkowski

On Fri, 8 Oct 2010, Elaine Meng wrote:

> 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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