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Hi Tim,
Grasp surfaces are defined via triangles. In fact, you can see how they
are defined in code a program called "ungrasp" that comes with the
Raster3D suite. Also, this is the specification from the (oldish) manual:
Grasp Surface File
This unformatted file starts with five "lines" of eighty
characters. The first line contains a format specifier, i.e. the words
"format=1". (There are no other formats at this time.) The second and
third lines contain key words for the information contained within, i.e.
"vertices" for the vertex positions, "accessible" for the associated
accessible surface point coordinates, "normals" for the normal vector
(of length unity) for each vertex, "triangles" for the triangle index
list. The latter is a list of integers such that entries i-2, i-1 and
i, where mod(i,3)=0, give the which vertices make up triangle i/3. NOTE
that the index integers for the triangles are INTEGER*2 ! Line three
contains which variable are also written to this file, "potentials",
"curvature", "distances", "gproperty1", "gproperty2" being the key words
for the appropriate quantities. Line four contains the number of
vertices, the number of triangles, the grid size of the lattice used to
create it (i.e. the number of points along one edge of the cube, always
=65), and the reciprocal lattice spacing. Line five contains the
midpoint of the coordinate system from which the vertices were derived
(i.e. the midpoint of the Grasp box). The data then follows in the
order of the keywords. Note that all are REAL*4 except for the triangle
indexes which are INTEGER*2.
Perhaps modifying a bit the ungrasp program would do the trick.
Cheers,
Miguel
En/na Tim Gruene ha escrit:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> This sounds quite reasonable - I do not know the grasp format, an sc only
> reads in grasp format. If it defines the surface via triangles and their
> order is not important, all you would have to do to invert the surface is
> to swap two points per triangle. This could be easily accomplished once
> the format of the grasp surface is known.
>
> Tim
>
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> On Thu, 22 Jun 2006, Miguel Ortiz-Lombardia wrote:
>
>> *** For details on how to be removed from this list visit the ***
>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>
>>
> Dear Tea and Tim,
>
> This may be a stupid idea, but what about this:
>
> 1. Superpose the proteins of interest
> 2. Compute their molecular surfaces with msms/Grasp or generate a mask
> with an appropriated probe
> 3. Take one of these surfaces and "invert it" over a cube defined from a
> clipping plane behind your region of interest (so the surface is put
> "inwards out" locally; for obvious reasons you cannot do this with all
> the surface)
> 4. Measure their complementarity with Michael Lawrence's "sc" program
> (in ccp4). You might need to translate stepwise if sc doesn't work on
> surfaces with clashes.
>
> Perhaps one of the tools to work with maps/mask could do the inversion?
>
> Or perhaps it's indeed a stupid idea, after all.
>
>
> Cheers,
>
>
>
>
> Miguel
>
>
> En/na Tim Gruene ha escrit:
>>>> *** For details on how to be removed from this list visit the ***
>>>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>>>
>>>>
>>>> You can use grasp or msms/Raster3D to calculate and visualise protein
>>>> surfaces.
>>>> But how would you _compare_ surfaces quantitatively?
>>>>
>>>> --
>>>> Tim Gruene
>>>> Institut fuer anorganische Chemie
>>>> Tammannstr. 4
>>>> D-37077 Goettingen
>>>>
>>>> GPG Key ID = A46BEE1A
>>>>
>>>>
>>>> On Wed, 21 Jun 2006, Tea Pavkov wrote:
>>>>
>>>>> *** For details on how to be removed from this list visit the ***
>>>>> *** CCP4 home page http://www.ccp4.ac.uk ***
>>>>>
>>>>>
>>>>> Dear ccp4bb,
>>>>>
>>>>> I would like to compare surfaces (not only ligand binding sites) of the
>>>>> proteins within the same family. Do you know if there is a program doing
>>>>> that or do you know people who are involved in developing something like
>>>>> that?
>>>>>
>>>>> Thank you in advance!
>>>>>
>>>>> Tea
>>>>>
>>>>>
>>>>> ---------------------------------------------------------
>>>>> Mag. Pavkov Tea
>>>>> Institute of Chemistry - Structural Biology
>>>>> Karl-Franzens-University Graz
>>>>> Heinrichstrasse 28, 8010 Graz, Austria
>>>>>
>>>>> Phone: ++43 316 380 5414
>>>>> Fax: ++43 316 380 9850
>>>>> http://PhysChem.kfunigraz.ac.at/sb
>>>>> ---------------------------------------------------------
>>>>>
> --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> e-mail: [EMAIL PROTECTED]
> ----------------------------------------------------------------------
> Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
> ce qui est fort fût juste.
> Blaise Pascal, Pensées
>>
- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
- ----------------------------------------------------------------------
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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