VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jan 12 2015 - 23:42:15 CST

Brian,
  If I've read your selection question correctly, I would suggest that
you try using the "withinbonds" selection keyword to solve your problem.
What about something like this (replace "ligand" with correct selection):
  ligand and oxygen and not withinbonds 1 of carbon

Cheers,
  John
  
On Mon, Jan 12, 2015 at 11:25:20PM -0600, John Stone wrote:
> 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/