[Chimera-users] FW: How to display H-bonds between atoms of selected residues ?

[Elaine Meng]

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 at 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 at 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 at 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