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

[Mahendra B Thapa]

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 at 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 at 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 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
>
>
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