>> 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,
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