Dear Dr. Elaine & Rama The hydrogen bonds related with a selected residue were displayed when I selected the option "with exactly one end selected". Thank you for help, Mahendra Thapa University of Cincinnati,OH On Wed, Oct 15, 2014 at 11:34 AM, Thapa, Mahendra (thapamb) < thapamb@mail.uc.edu> wrote:

________________________________________ From: Elaine Meng Sent: Wednesday, October 15, 2014 9:34:43 AM (UTC-06:00) Central America To: Thapa, Mahendra (thapamb) Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] FW: How to display H-bonds between atoms of selected residues ?

Dear Mahendra, First, you would select residue 291. There are many ways to select. One way is to Ctrl-click to select some atom or bond in that residue and then press up arrow on your keyboard one time to select the whole residue. Another way is to show Sequence (menu Favorites… Sequence) and drag a box on just that residue in the sequence, which will select it in the structure.

Then if you are using the FindHBond dialog (in menu under Tools… Structure Analysis), there is an option in dialog that you need to turn on, "Only find H-bonds", with additional choices: with at least one end selected with exactly one end selected with both ends selected between selection and atom spec…

You can click the Help button on FindHBond to see the full manual page.

If you are using the "findhbond" command, there is a "selRestrict" option to do the same things. Use command "help findhbond" to see the possible values of that option.

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 15, 2014, at 8:09 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:

...

Hi, Rama

I tried by selecting the residue, but still all hydrogen bonds were displayed as before. I just want to display H-bonds related with the residue only.

Thank you for help, Mahendra Thapa University of Cincinnati,OH

On Wed, Oct 15, 2014 at 2:56 AM, Thapa, Mahendra (thapamb) < thapamb@mail.uc.edu> wrote:

From: rama david Sent: Wednesday, October 15, 2014 12:56:19 AM (UTC-06:00) Central America To: Thapa, Mahendra (thapamb) Subject: Re: [Chimera-users] How to display H-bonds between atoms of selected residues ?

Dear Sir, You first select the residue and then go in structure analysis tools I think this should work fine. If this not work then let it know please

best wishes,

On Wed, Oct 15, 2014 at 11:56 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote: Dear Chimera Users,

By using 'Structure analysis tool' of Chimera, all possible H-bonds between atoms were displayed.

I am interested to display only H-bonds between atoms of selected residues, say H-bonds between atoms of residue number 291 and atoms of rest of the residues including atoms of residue 291 in a pdb file with 300 residues. Any suggestion definitely helps me a lot.

Thank you, Mahendra Thapa University of Cincinnati,OH