VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Sat Sep 10 2011 - 00:49:34 CDT

Error message. I was just sent a suggestion that didn't work either- it did show the desired residues on one of the chains, but ALL of the other chain. That inspired me to some transmogrifications, of which(all within 5 of chain B) and (all within 5 of chain A) did what I wanted. Thanks so much for the help!Irene
> Date: Fri, 9 Sep 2011 21:27:25 -0400
> Subject: Re: vmd-l: Displaying residues on chain A within X of chain B
> From: akohlmey_at_gmail.com
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> On Fri, Sep 9, 2011 at 8:54 PM, Irene Newhouse <einew_at_hotmail.com> wrote:
> > Thanks! I just tried that & it doesn't work.
>
> doesn't work in which way?
>
> error message, or showing the wrong atoms?
>
> axel.
>
> > Irene
> >
> >> Date: Fri, 9 Sep 2011 18:51:33 -0400
> >> Subject: Re: vmd-l: Displaying residues on chain A within X of chain B
> >> From: akohlmey_at_gmail.com
> >> To: einew_at_hotmail.com
> >> CC: vmd-l_at_ks.uiuc.edu
> >>
> >> On Fri, Sep 9, 2011 at 5:19 PM, Irene Newhouse <einew_at_hotmail.com> wrote:
> >> > I'm trying to display the residues 'contacting' chain A on chain B of a
> >> > protein [I'd be satisfied with setting a distance, as one does with
> >> > 'within'] & I can't get the selection language to work in the graphical
> >> > representations window. I've done some searching of the VMD-L archive,
> >> > since
> >> > people must want to do this, but I don't seem to have found the magic
> >> > search
> >> > terms. Using residue number isn't obvious, as the residues aren't
> >> > numbered
> >> > consecutively throughout the pdb file, but restart with each chain.
> >>
> >> irene,
> >>
> >> have you tried "same residue as (chain A exwithin ##.# of chain B)" ?
> >>
> >> cheers,
> >> axel.
> >>
> >>
> >> > Thanks!
> >> > Irene Newhouse
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>