VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 29 2005 - 10:02:11 CST

Josh,
  Are you certain that those two structures that only return 46 CA indices
don't have some naming issue etc? Can you send me the structure files for
all of the molecules in question?

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 29, 2005 at 10:36:39AM -0500, Josh Ward wrote:
> I initially had that idea as well, but when I replaced "alpha" with
> "name CA" the problem persists. I'm still confused.
>
> Main console display active (Tcl8.4.1 / Tk8.4.1)
> (martin) 37 % set a0 [atomselect 0 "name CA"]
> atomselect0
> >Main< (martin) 38 % set a1 [atomselect 1 "name CA"]
> atomselect1
> >Main< (martin) 39 % set a2 [atomselect 2 "name CA"]
> atomselect2
> >Main< (martin) 40 % set a3 [atomselect 3 "name CA"]
> atomselect3
> >Main< (martin) 41 % set a4 [atomselect 4 "name CA"]
> atomselect4
> >Main< (martin) 42 % llength [$a0 get index]
> 106
> >Main< (martin) 43 % llength [$a1 get index]
> 106
> >Main< (martin) 44 % llength [$a2 get index]
> 46
> >Main< (martin) 45 % llength [$a3 get index]
> 106
> >Main< (martin) 46 % llength [$a4 get index]
> 46
> >Main< (martin) 47 %
>
>
> John Stone wrote:
>
> >Josh,
> > The atom selection keyword "alpha" depends on the secondary structure.
> >VMD gets the secondary structure for a molecule by running the STRIDE
> >program, which calculates it heuristically, based on the 3-D structure.
> >It is quite possible that the reason you're having trouble is because
> >STRIDE is assigning a differing number of atoms as alpha helices in the
> >various structures you've got. You can see that's what's going on by
> >comparing the atom counts as you did below. Given this result, I'd
> >suggest changing your alignment script to use a selection such as
> >"name CA" or something of that sort. Otherwise, another way to solve
> >the problem is to extract the list of atom indices from the "alpha"
> >selection for your zeroth molecule, make a new atom selection macro
> >from that list of indices, and then use the macro to select the same
> >set of atoms for all molecules, and that will solve your problem.
> >The issue here is just that when you used the "alpha" selection, you're
> >relying on STRIDE to make exactly the same secondary structure prediction
> >for all of your molecules, which as you can see it won't necessarily do.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Thu, Mar 24, 2005 at 04:49:44PM -0500, Josh Ward wrote:
> >
> >
> >>I think I have found a MOLID-dependent bug in atomselection using TCL.
> >>I'm running VMD 1.8.3 on Debian Sarge Linux with TCL 8.4.1 / TK8.4.1
> >>
> >>I have three structures of the same protein in charmm crd format that I
> >>am trying to align. Each loaded seperately - result = molids 0, 1, and
> >>2 are used. When I tried to align, molid 0 and molid 1 align without
> >>problem, but tcl complains that the number of selected atoms differes
> >>between 0 and 2.
> >>
> >>After double checking the integrety of the crd file, I loaded a single
> >>file multiple times and tried to realign, getting the same error
> >>result. Loading the same file 5 times and trying to align, I got the
> >>following output in the TK console:
> >>
> >>Main console display active (Tcl8.4.1 / Tk8.4.1)
> >>37 % set a0 [atomselect 0 "alpha"]
> >>atomselect0
> >>
> >>
> >>>Main< 38 % set a1 [atomselect 1 "alpha"]
> >>>
> >>>
> >>atomselect1
> >>
> >>
> >>>Main< 39 % set a2 [atomselect 2 "alpha"]
> >>>
> >>>
> >>atomselect2
> >>
> >>
> >>>Main< 40 % set a3 [atomselect 3 "alpha"]
> >>>
> >>>
> >>atomselect3
> >>
> >>
> >>>Main< 41 % set a4 [atomselect 4 "alpha"]
> >>>
> >>>
> >>atomselect4
> >>
> >>
> >>>Main< 42 % llength [$a0 get index]
> >>>
> >>>
> >>106
> >>
> >>
> >>>Main< 43 % llength [$a1 get index]
> >>>
> >>>
> >>106
> >>
> >>
> >>>Main< 44 % llength [$a2 get index]
> >>>
> >>>
> >>43
> >>
> >>
> >>>Main< 45 % llength [$a3 get index]
> >>>
> >>>
> >>106
> >>
> >>
> >>>Main< 46 % llength [$a4 get index]
> >>>
> >>>
> >>43
> >>
> >>
> >>>Main< 47 %
> >>>
> >>>
> >>This alignment procedure worked until we upgraded to 1.8.3 I'm not sure
> >>if the bug might be in TCL. It won't align when I downgrade to 1.8.2
> >>either.
> >>
> >>Thanks in advance,
> >>Josh
> >>
> >>--
> >>Josh Ward
> >>Graduate Research Assistant
> >>Purdue University
> >>Department of Medicinal Chemistry and Molecular Pharmacology
> >>Lily Hall of Life Sciences
> >>Phone: (765) 494-2191
> >>
> >>
> >
> >
> >
>
> --
> Josh Ward
> Graduate Research Assistant
> Purdue University
> Department of Medicinal Chemistry and Molecular Pharmacology
> Lily Hall of Life Sciences
> Phone: (765) 494-2191 

-- 
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