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*** CCP4 home page http://www.ccp4.ac.uk ***
People interested in molecular surface and volume calculations should
probably look into the alpha shapes software. Jie Liang and Herbert
Edelsbrunner wrote one version (VOLBL and its associated programs) and
another, more modern version by Patrice Kohl (I forget the names, I think
it is called Proshape or something like that. Kohl is at UC Davis now,
and was at Stanford). He's very friendly if you have questions.
Both of those packages should give you things like volume and surface per
residue.
(Many thanks to Richard Gillilan for originally pointing these out to me.)
Cheers,
Marcus Collins
*****************************************************************************
Marcus D. Collins
Gruner Biophysics Group, Cornell University Dept. of Physics, LASSP
(h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650
"You have opened a new door, and I share this with you,
for I have been where you are now."
*****************************************************************************
On Fri, 30 Sep 2005, Erwin De Genst wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Hi,
>
> I was following this discussion with interest since I am desperately looking
> for a program that calculates molecular surfaces. As I understand it
> 'areaimol' or 'surface' cannot calculate this because they do not calculate
> completely the surface described by the locus of the inward-facing probe
> sphere (the reentrant surface is lacking). Does anyone know if there is a
> program that calculates molecular surfaces and which gives an output per
> residue?
>
> Erwin
> >
> >Thanks all for your helpful replies.
> >
> >I found the article mentioned very useful,
> >
> >http://www.ccp4.ac.uk/newsletters/newsletter38/03_surfarea.html
> >
> >
> >My major problems started when I confused the 'contact area' with the
> >'area in contact' for a subunit in an oligomer, but now I understand
> >that areaimol doesn't compute that directly. It would be really nice if
> >the man page for areaimol pointed to the above article.
> >
> >Cheers,
> >Dan.
> >
> >
> >
> >[EMAIL PROTECTED] wrote:
> >> *** For details on how to be removed from this list visit the ***
> >> *** CCP4 home page http://www.ccp4.ac.uk ***
> >>
> >>
> >>
> >> Hello,
> >>
> >> I recently started using 'areaimol' in the CCP4 program suite,
> >>
> >> CCP4 5.0
> >> AREAIMOL 5.0
> >> 30/01/04
> >>
> >> I am using default settings to look at 'simple area calculation' of a
> >> protein. The results file has two major sections,
> >>
> >> 1) ACCESSIBLE AREAS (for the residue/chain/oligomer)
> >> 2) CONTACT AREAS (for the residue/chain/oligomer)
> >>
> >> What is the difference between these two measures? (Are they even related
> >> measures, or do they measure different physical properties of the
> >> molecule?)
> >>
> >> From the manual I read...
> >>
> >> "The contact area is defined as the area on the Van der Waals surface of
> >> an atom that can be contacted by a sphere of the given probe radius."
> >>
> >> but that sounds just like the ASA?
> >>
> >> I am a beginner with these concepts, so I don't see how (if at all) the
> >> two measures are related, or why two measures are needed.
> >>
> >> Thanks for any help,
> >>
> >> Dan.
> >>
> >>
> >>
> >>
> >
> >
> >
> >
>
>
