VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon May 03 2004 - 10:14:02 CDT

Hi Ahmet,

Just add another qualifier in your selection statement or lsort the list
that "connected" gives you.

ie..

 set connected [atomselect top "(same residue as ([$HATOM text])) and
nitrogen"]

Regards,
Brian

On Mon, 3 May 2004, Ahmet Bakan wrote:

> Hi Justin and All,
>
> I need the index of the single atom that hydrogen is bonded to.
> Like this
> -NH-CH2-CO-O-
> I have the index of H bonded to N, hundereds of H similar indices.
> I need index of N atom in this example.
>
> I tried this:
> set HATOM [atomselect top "index 547"]
> Result: H
> set connected [atomselect top "same residue as ([$HATOM text])"]
> Result: NH1 H CT1 HB CT2 HA HA CT2 HA HA CC O NH2 H H C O
> set connected [atomselect top "same bond as ([$HATOM text])"]
> Result: nothing happens
>
> Does anyone have idea?
> Thanks,
>
> Ahmet
>
>
> ==========ABC==========
> Ahmet Bakan
> Chemistry, Junior
> Koc University
> abakan_at_ku.edu.tr
> ICQ #86167698
> http://home.ku.edu.tr/~abakan
>
> -----Original Message-----
> From: Justin Gullingsrud [mailto:jgulling_at_mccammon.ucsd.edu]
> Sent: Monday, May 03, 2004 11:36 AM
> To: Ahmet Bakan
> Cc: VMD-L
> Subject: Re: vmd-l: Selection problem on TkCon
>
> Hi,
>
> On Mon, May 03, 2004 at 03:55:43AM +0300, Ahmet Bakan wrote:
> > Hi All,
> >
> >
> >
> > I have a selection of Hydrogen atoms and I want to get the list of atoms
> > that Hydrogens in my selection are attached to. How can this be done on
> > TkCon?
>
> I assume you have a selection that you created from the text console,
> something like this:
>
> set sel [atomselect top "hydrogen and resname ALA"]
>
> Whatever the selection is, you can find all the atoms in the same
> residue as the selection by typing the following:
>
> set connected [atomselect top "same residue as ([$sel text])"]
>
> You can then write out a list of atoms in the selection to a file with:
>
> set fd [open connatoms.ind w]
> foreach ind [$connected list] { puts $fd $ind }
> close $fd
>
> Note that the indicies written to the file will be one smaller than the
> corresponding atom in a pdb file; i.e., they will be 0-based rather than
> 1-based.
>
> Cheers,
> Justin
>
> >
> >
> >
> > Cheers,
> >
> > Ahmet
> >
> >
> >
> > ==========ABC==========
> >
> > Ahmet Bakan
> >
> > Chemistry, Junior
> >
> > Koc University
> >
> > abakan_at_ku.edu.tr
> >
> > ICQ #86167698
> >
> > http://home.ku.edu.tr/~abakan
> >
> >
> >
>
> --
>
> Tenth is 10 spots too low as far as I'm concerned. -- George W. Bush
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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