SPDV

Simon Andrews simon.andrews at bbsrc.ac.uk
Mon May 22 12:54:23 EST 2000


dawe wrote:
> 
> Does anybody knows Swiss PDB viewer? Can anybody explain how to calculate
> the surface of a part of the molecule. I've tried by selecting the
> interested part, but it displays the whole surface..

What kind of surface do you want?  For van der Waals or solvent
accessible surfaces simply select the residues you are interested in,
then select the surface type you want by clicking on the small " V "
under the column in the control panel which is headed  :: .  Then click
on the " :: " header itself.  That suface will then be applied to the
selected residues.

For a molecular surface there are two approaches you can take;

1) Select no residues.  Calculate a full molecular surface using Tools
-> Compute molecular surface.  Select the residues you are interested
in.  Select the molecular surface type as described above, then click on
the :: sign in the Control Panel to view the surface only for the
selected residues.

This will show you the partial surface for a group of selected
residues.  It will not show a surface around residues which were not
originally on the exterior of the protein.

Alternatively;

2) Go to Preferences -> Surfaces.  Check that the box which says "Ignore
Selected Residues" is ticked.  Select the residues you are interested
in.  Inverse your selection (Select -> Inverse Selection) so that
everything you are *not* interested in is selected.  Calculate the
surface with Tools -> Compute molecular surface.

This will provide the molecular surface for the subset of residues you
were interested in.  This surface is created as if the rest of the
groups did not exist.


I hope this helps


Simon.






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