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.
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.
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.
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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.
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_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Forbes, AddH is not minimizing an energy function. It does attempt to avoid clashes, and by default ("also consider H-bonds") also to add the hydrogens of hydroxyls at positions that enable hydrogen-bonding, but the process is neither combinatorial nor an optimization. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> "Although hydrogens are placed to avoid clashes and form hydrogen bonds where possible, they are not energy-minimized, and a globally optimal network in terms of the number of H-bonds or total H-bonding energy is not necessarily found." The hydrogens are added using the bond lengths from the Amber force field (parm99 prameter set), shown in a table in the help page (URL above). For a more intensive approach to adding hydrogens, you could try the Reduce program from the Richardson Laboratory. A more detailed description and some links are provided in the bottom section of the AddH help page. Best, 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 28, 2010, at 7:13 AM, Forbes J. Burkowski wrote:
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
participants (3)
-
Elaine Meng -
Forbes J. Burkowski -
Peter Baker