VMD-L Mailing List
From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Tue Jan 13 2015 - 11:05:22 CST
Sounds like a virtual screeen.
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Bennion, Brian [bennion1_at_llnl.gov]
Sent: Tuesday, January 13, 2015 10:04 AM
Subject: RE: vmd-l: Re: FW: atomselection by wildcard and distance exclusion
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.
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?
> -----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
> Whatever is going amiss that caused your email truncation
> seems to have occured twice in a row now. Let's see if this reply
> it through unscathed or not, and then we can work on the selection
> 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
> > sentence. The text below was want was sent to me and cc'ed to the
> > 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
> > 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
> > carbon. My ligand has oxygen atoms bound to nitrogen, hydrogen,
> > 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
> > 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
> > because my selection text is not returning what I expect to be the
> > 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
> > I want to eliminate all oxygen atoms bound to carbon:
> > set oxime [atomselect top "resname LIG and name \"O.*\" and same
> > 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