Growing and shrinking algorithm

Gerard Kleywegt gerard at xray.bmc.uu.se
Thu May 23 00:25:51 EST 1996


In article <1996May21.143324.38315 at ucl.ac.uk>, bob at bsm.bioc.ucl.ac.uk (Bob
MacCallum) wrote:

?> Hello,
?> 
?> I've been using an incremental growing and shrinking algorithm (within
?> GRASP if you must know) in order to smooth out a jagged and discontinuous
?> surface patch.  It's all pretty common sense really: you just grow your
?> patch by 1 angstrom 5 times, and then shrink it 5 times by 1 angstrom and
?> hey presto it works.
?> 
?> My major problem is finding a reference to this concept.  Can you help?
?> 
?> I vaguely remember a paper which eliminated internal (water) cavities in
?> protein structures using just this method (in three dimensions).  But I
?> can't find it, in my filing cabinet or in the bibliographic database
?> (although it is a difficult to search for).
?> 
?> I would be very grateful if anyone could help.  I can pass on the macros if
?> anyone's interested.
?> 
?> cheers
?> 
?> Bob.
?> 

we've used it in VOIDOO to delineate cavities that are in contact with the
"outside world"; GJK & TA Jones, Acta Cryst D50, 178-185 (1994)

we also use it in our mask-editing program MAMA in order to smooth
molecular envelopes (for density averaging); GJK & TAJ, CCP4 Proceedings
of 1994, pp. 59-66

i'm sure i was standing on the shoulders of giants when i programmed
these things, i.e. other people must have thought of it before, although
i don't have any references

(how did that quote go again ? "if i haven't seen as far as others, it was
because giants were standing on my shoulders" ? ;-)

?> --
?> ++++++++++++++++++++++++++++++ Bob MacCallum ++++++++++++++++++++++++++++++
?> +++++++++++++++ Biomolecular Structure and Modelling Group ++++++++++++++++
?> ++++++++++++ Department of Biochemistry and Molecular Biology +++++++++++++
?> ++++++++++++++++ University College London, WC1E 6BT, UK ++++++++++++++++++

--cd
--------------------------------------------------------------------
Gerard J. Kleywegt
Department of Molecular Biology, Biomedical Centre
Uppsala University, Uppsala, SWEDEN




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