Hi: 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@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users