Root mean square distance between two known structures?

bionet at cgmvax.cgm.cnrs-gif.fr bionet at cgmvax.cgm.cnrs-gif.fr
Thu Mar 18 03:53:58 EST 1993

> In article <113595 at netnews.upenn.edu> duong at chestnut.chem.upenn.edu (Duc Duong)
>  writes:
> >
> >hi..
> >
> >does any one know a software (PD or commercial) that will compare 3D
> >structures of two proteins by measuring minimum possible root mean
> >square bwetween equivalent C alpha positions?
> >

 An answer by R. Ketchen was:
> You could write the code yourself with the following information:
> First the two structures must be superimposed. See:
> Kearley, S.K., J. Comput. Chem., 11, 1187-1192 (1990).
> Next you can calculate the distances between atoms (in C) with:
> d = sqrt(pow(atom1[X] - atom2[X], 2)
>        + pow(atom1[Y] - atom2[Y], 2)
>        + pow(atom1[Z] - atom2[Z], 2));
> Square all of the distances, average the squares, and take the square root.
> That's all!

        I'm afraid the problem is not so much to calcultate the RMS distance
 between equivalenced C-alpha's, but first to calculate the rotation+
 translation matrices which will superimpose at best the equivalent C-alpha's.
        For this purpose, I use an excellent (fast and efficient) routine
 written in FORTRAN by Wolfgang KABSCH who used to work at the Max-Planck
 Institut at Heidelberg. I apologize for not knowing his E-mail address, but
 I'm sure that those people working at the EMBL who read this B-Board will
 know it and will forward it (I am reluctant to send Kabsch's routine by mail
 without his permission).

        See the references: Acta Crystallogr. A34 (1978) 827-828
                            Acta Crystallogr. A32 (1976) 922-923

 Best of luck,

 | Jean-Loup Risler                   |                               |
 | CNRS                               | risler at frcgm51.bitnet         |
 | Centre de Genetique Moleculaire    | risler at cgmvax.cgm.cnrs-gif.fr |
 | 91198  Gif sur Yvette Cedex France |                               |

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