Subject: Re: CCL:Problem with Kabsch measure for RMSD on planar molecules

From: "Alexandre Suman de Araujo" <[email-masked]>
Date: Thu, 18 Jul 2002 09:28:02 -0300

I made a program that implement Kabsch algorithm in a visual windows
program. It's free, but it's a beta version yet. If you want a copy, send me
a e-mail and I'll send it to you... ok???!!!

Alexandre Suman de Araujo
IFSC - USP - São Carlos
UIN: 6194055
----- Original Message -----
From: "Paul Darwen" <[email-masked]>
To: <[email-masked]>
Sent: Wednesday, July 17, 2002 9:36 PM
Subject: CCL:Problem with Kabsch measure for RMSD on planar molecules

>
> I have a problem with the Kabsch method of measuring root-mean-square
> distance (RMSD) between molecules, as described in Kabsch 1978, Acta
> Cryst A34:827-828.
>
> As far as I can make out, the Kabsch method works so long as three
> or more planes are needed to intersect all the atoms.  This means
> that if a molecule happens to (say) be in a single flat plane, then
> the Kabsch method chokes.
>
> For example, consider a molecule that's two carbon rings joined by
> a bridge.  This makes it flat.
>
> Below are two Sybyl2 copies of this molecule, but rotated and translated.
> Their root-mean-square distance (RMSD) after alignment should be zero.
>
> But running Tinker's "superpose" program will align them lengthwise,
> but they're still rotated about the lengthwise axis and not aligned.
> The same thing happens in VMD if you try to align them with the script
>    /usr/local/lib/vmd/scripts/vmd/rmsd.tcl
> Both of these incorrectly return an RMSD that's way more than zero.
>
> Has anyone written an RMSD measure that copes with planar molecules
> like this?  If you can run the following two molecules through your
> align-and-measure-RMSD routine and get zero for an answer, I'd be
> grateful for a copy.
>
> __________________________________________________________________
>
> Paul Darwen                          www.protagonist.com.au/darwen
> Protagonist Pty Ltd                      [email-masked]
> Brisbane 4064 Australia                     Phone: +61-7-3377-0304
>
>
> --------------- This is the first of two molecules ---------------
>
> @<TRIPOS>MOLECULE
> Bridge bond between two carbon rings
>       22      23       1
> SMALL
> NO_CHARGES
>
> @<TRIPOS>ATOM
>        1   C1           1.304260    1.349055   -0.389125   C.2
>        2   C2           1.980455    0.216229   -0.145061   C.2
>        3   C3           1.892984   -0.380446    1.046579   C.2
>        4   C4           1.123138    0.166682    1.990862   C.2
>        5   C5           0.447667    1.299539    1.744975   C.2
>        6   C6           0.512887    1.932896    0.546310   C.2
>        7   H7          -0.161845    1.681260    2.577240   H
>        8   H8           1.043615   -0.318373    2.979753   H
>        9   H9           2.448954   -1.312367    1.248134   H
>       10   H10          2.614125   -0.227590   -0.933089   H
>       11   H11          1.432842    1.773440   -1.395729   H
>       12   C12         -0.113409    3.725645   -0.903027   C.2
>       13   C13         -0.788738    4.858585   -1.148921   C.2
>       14   C14         -1.558584    5.405739   -0.204656   C.2
>       15   C15         -1.646220    4.808998    0.986939   C.2
>       16   C16         -0.970147    3.676100    1.230993   C.2
>       17   C17         -0.178748    3.092243    0.295605   C.2
>       18   H18         -1.098820    3.251664    2.237563   H
>       19   H19         -2.279900    5.252856    1.774946   H
>       20   H20         -2.114383    6.337763   -0.406164   H
>       21   H21         -0.709092    5.343685   -2.137780   H
>       22   H22          0.496097    3.343872   -1.735268   H
>
> @<TRIPOS>BOND
>        1       1       2       1
>        2       1       6       1
>        3       1      11       1
>        4       2       3       1
>        5       2      10       1
>        6       3       4       1
>        7       3       9       1
>        8       4       5       1
>        9       4       8       1
>       10       5       6       1
>       11       5       7       1
>       12       6      17       1
>       13      12      13       1
>       14      12      17       1
>       15      12      22       1
>       16      13      14       1
>       17      13      21       1
>       18      14      15       1
>       19      14      20       1
>       20      15      16       1
>       21      15      19       1
>       22      16      17       1
>       23      16      18       1
>
> @<TRIPOS>SUBSTRUCTURE
>        1            ****       1
>
>
> --------------- This is the second of two molecules ---------------
>
> @<TRIPOS>MOLECULE
> Bridge bond between two carbon rings
>       22      23       1
> SMALL
> NO_CHARGES
>
> @<TRIPOS>ATOM
>        1   C1           0.054840    0.525138   -1.730657   C.2
>        2   C2           1.112013   -0.267815   -1.962393   C.2
>        3   C3           2.327386    0.082664   -1.533765   C.2
>        4   C4           2.474774    1.233137   -0.871667   C.2
>        5   C5           1.416448    2.024847   -0.640943   C.2
>        6   C6           0.167392    1.700650   -1.061558   C.2
>        7   H7           1.626775    2.952893   -0.089236   H
>        8   H8           3.475262    1.532683   -0.512794   H
>        9   H9           3.197548   -0.569107   -1.724045   H
>       10   H10          0.978844   -1.216950   -2.510944   H
>       11   H11         -0.908118    0.160964   -2.117910   H
>       12   C12         -0.802543    3.687019   -0.155836   C.2
>       13   C13         -1.859722    4.479966    0.075891   C.2
>       14   C14         -3.075096    4.129477   -0.352705   C.2
>       15   C15         -3.222482    2.979014   -1.014814   C.2
>       16   C16         -2.164151    2.187340   -1.245587   C.2
>       17   C17         -0.915090    2.511520   -0.824932   C.2
>       18   H18         -2.374444    1.259272   -1.797273   H
>       19   H19         -4.223035    2.679500   -1.373569   H
>       20   H20         -3.945250    4.781258   -0.162414   H
>       21   H21         -1.726500    5.429133    0.624380   H
>       22   H22          0.160424    4.051217    0.231410   H
>
> @<TRIPOS>BOND
>        1       1       2       1
>        2       1       6       1
>        3       1      11       1
>        4       2       3       1
>        5       2      10       1
>        6       3       4       1
>        7       3       9       1
>        8       4       5       1
>        9       4       8       1
>       10       5       6       1
>       11       5       7       1
>       12       6      17       1
>       13      12      13       1
>       14      12      17       1
>       15      12      22       1
>       16      13      14       1
>       17      13      21       1
>       18      14      15       1
>       19      14      20       1
>       20      15      16       1
>       21      15      19       1
>       22      16      17       1
>       23      16      18       1
>
> @<TRIPOS>SUBSTRUCTURE
>        1            ****       1
>
> --------------- End of the second of two molecules ---------------
>
>
>
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