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Re: [ccp4bb]: Protein Dimensions



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On Wed, 20 Feb 2002, Luca Jovine wrote:

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> >What is the best way to determine a proteins dimensions from the three
> >dimensional structure?  I could just measure from end to end at the
> >widest point (between CA's) in Xfit, but is there a better method that
> >would take into account a Van der Waals surface or something similar.
>
> There might be better ways, but:
>
> 1) within CNS, you can use the input file molecule_extent.inp, which
> "Determines the extent of a molecule in orthogonal Angstroms"
>
> 2) in WHATIF, you can use the command MINMAX which determines the
> extreme values for the coordinates within a user-specified range
>
> Hope this helps, Luca

The problem with this method is that the answer depends on the orientation of
your molecule which is normally not what you want. Depending on the molecule
of interest there can be different dimensions that would be of interest (e.g.
dimention parallel to a dimer axis). However, in general I think you want to
find the principle axes. E.g. the longest dimension, the longest dimension
perpendicular to the first one, and the dimension perpendicular to the other
two. There may be a dedicated program for that but the only thing that comes
to mind is the TABFUN step of AMORE. Here the program rotates the molecule so
that its principal axes are aligned with the x, y, and z axes and it then
gives the minimal box which should correspond to the dimensions of the protein
(check to make sure it doesn't add an small amount to the numbers by running
the produced PDB file through any programs that calculate the extend of the
molecule (or use unix "sort" to sort on the x, y, and z columns to find the
extreme values).

Bart

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