VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 13 2015 - 10:18:15 CST

Brian,
  Did you try my 'withinbonds' suggestion yet?

Cheers,
  John

On Tue, Jan 13, 2015 at 04:04:52PM +0000, Bennion, Brian wrote:
> Hello Norman
>
> This would work for one ligand and would be ideal if I could control the atom labeling up stream from my work. I have hundreds of ligands and unfortunately they do not keep the same atom labels.
>
> Brian
>
>
> ________________________________________
> From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Norman Geist [norman.geist_at_uni-greifswald.de]
> Sent: Monday, January 12, 2015 11:27 PM
> To: 'John Stone'
> Cc: VMD Mailing List
> Subject: AW: vmd-l: Re: FW: atomselection by wildcard and distance exclusion
>
> Given the fact that atom names are unique within a residue, why not use atom
> names for the selection?
>
> Norman Geist.
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von John Stone
> > Gesendet: Dienstag, 13. Januar 2015 06:25
> > An: Bennion, Brian
> > Cc: vmd-l_at_ks.uiuc.edu
> > Betreff: vmd-l: Re: FW: atomselection by wildcard and distance
> > exclusion
> >
> > Brian,
> > Whatever is going amiss that caused your email truncation
> > seems to have occured twice in a row now. Let's see if this reply
> > makes
> > it through unscathed or not, and then we can work on the selection
> > issue.
> >
> > Cheers,
> > John Stone
> >
> > On Tue, Jan 13, 2015 at 05:12:58AM +0000, Bennion, Brian wrote:
> > > Hello All, I am not sure why my last email was truncated after the
> > first
> > > sentence. The text below was want was sent to me and cc'ed to the
> > vmd-l
> > > list.
> > >
> > > ------------------------------------------------------------------
> > ---------
> > >
> > > From: Bennion, Brian
> > > Sent: Monday, January 12, 2015 4:57 PM
> > > To: vmd-l_at_ks.uiuc.edu
> > > Subject: atomselection by wildcard and distance exclusion
> > > Hello All,
> > >
> > > After working on this for far too long I need to know what I am
> > doing
> > > wrong.
> > >
> > > I have a pdb file that contains a protein and a docked ligand. I
> > want to
> > > select one or more oxygen atoms on the ligand that is not bound to
> > a
> > > carbon. My ligand has oxygen atoms bound to nitrogen, hydrogen,
> > and/or
> > > hydrogen.
> > >
> > > There are two possible procedures one might explore to make the
> > > atomselection.
> > >
> > > One might look at all the oxygen atoms and get a list of index
> > values for
> > > each atom that is returned in the lists from the atomselect0
> > getbonds
> > > command and check for whether it is a carbon or not.
> > > This might be called the analytical solution because if you
> > iterate enough
> > > you should get an atomselection that contains an oxygen atom that
> > does not
> > > have any bonds with a carbon atom.
> > > Honestly I got lost in the foreach recursive searches.
> > >
> > > Second is a numerical approach that uses a distance constraint to
> > > eliminate the selection of oxygen atoms that have other atoms
> > within 1.5
> > > angstrom.
> > > I concentrated on this approach and obviously need to learn
> > something
> > > because my selection text is not returning what I expect to be the
> > correct
> > > result. Obviously it is just doing what I told it to do.
> > >
> > > One ligand molecule has 3 oxygen atoms. One oxygen is bound to
> > two carbon
> > > atoms with bond distances of <1.45A. One oxygen double bonded to
> > a carbon
> > > and the final oxygen atom is bound to a nitrogen and hydrogen
> > atom.
> > >
> > > I want to eliminate all oxygen atoms bound to carbon:
> > > set oxime [atomselect top "resname LIG and name \"O.*\" and same
> > residue
> > > as not within 1.5 of name \"C.*\" "]
> > >
> > > The command returns three oxygen atoms.
> > > My logic is flawed in the selection text.
> > > Any pointers to fix this?
> > >
> > > Thank you
> > > Brian Bennion
> >
> > --
> > NIH Center 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/
>
> 

-- 
NIH Center 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/