VMD-L Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Oct 31 2011 - 17:03:55 CDT

two thing immediately come to mind:
1) can you re-start vmd, but without your customized .vmdrc and retry?

2) I know this will sound patronizing, and I apologize, but we must
check: are you sure that 12 A radius doesn't encompass your entire system? It
would be 12 A from the farthest edges of your selection.

Best,
Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
matziast_at_med.uth.gr writes:
> Date: Mon, 31 Oct 2011 23:15:54 +0200
> From: matziast_at_med.uth.gr
> To: John Stone <johns_at_ks.uiuc.edu>
> Cc: Chris Harrison <charris5_at_gmail.com>, vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: selection
> User-Agent: Internet Messaging Program (IMP) H3 (4.0.3)
> 
> Hi,
> you are right, sorry. Both of the two ways:
> (proteinback or nucleicback) and not within 12 of resname X and
> backbone and not (within 12 of resname X) gave the same result, all atoms were
> fixed. I checked VMD, it recognizes correctly the structure.
> Thank you in advance,
> Maria.
> 
> Quoting John Stone <johns_at_ks.uiuc.edu>:
> 
> >
> >Hi,
> > Are you sure that VMD is correctly recognizing your structure
> >in the first place?  Do you see what you expect to see if you
> >just select "protein", or "not protein", "backbone", and "not backbone"
> >for example?  If you expect people to help you, you'll have to give
> >more feedback on what results you got than simply "it was not the solution".
> >What remained incorrect after you tried the suggestions people gave you?
> >Be specific.
> >
> >Cheers,
> > John
> >
> >On Mon, Oct 31, 2011 at 10:57:03PM +0200, matziast_at_med.uth.gr wrote:
> >>Unfortunately it was not the solution.
> >>
> >>
> >>Quoting Chris Harrison <charris5_at_gmail.com>:
> >>
> >>>backbone and not (within 12 of resname X))
> >>>
> >>>Best,
> >>>Chris
> >>>
> >>>
> >>>--
> >>>Chris Harrison, Ph.D.
> >>>Theoretical and Computational Biophysics Group
> >>>NIH Resource for Macromolecular Modeling and Bioinformatics
> >>>Beckman Institute for Advanced Science and Technology
> >>>University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
> >>>
> >>>char_at_ks.uiuc.edu                          Voice: 773-570-0329
> >>>http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
> >>>
> >>>
> >>>matziast_at_med.uth.gr writes:
> >>>>Date: Mon, 31 Oct 2011 19:45:50 +0200
> >>>>From: matziast_at_med.uth.gr
> >>>>To: vmd-l_at_ks.uiuc.edu
> >>>>Subject: vmd-l: selection
> >>>>User-Agent: Internet Messaging Program (IMP) H3 (4.0.3)
> >>>>
> >>>>Hi,
> >>>>I want to select only the protein backbone and the nucleic backbone and
> >>>>not
> >>>>within 12 or resname X.
> >>>>For that reason I type "proteinback or nucleicback and not within 12
> >>>>of resname
> >>>>X"
> >>>>but the final selection included all proteins and backbone. Why?
> >>>>I would appreciate if anyone could help me.
> >>>>Thank you in advance.
> >>>
> >>
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
> >http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078
> >
> 
>