Dear Pietro, On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi <pietro.rove...@path.ox.ac.uk> wrote:
> Dear everyone, > I want to represent a domain of my molecule as a low > resolution solid shape. > > I have chosen surface representation but the surface is clipped, > exposing the inner part, which makes the domain appear hollow. The > rendering of the inner surface appears greyish and different from the > outer part. > > Can I make the clipped surface filled so that this greyish inner part is > not there anymore? It should look solid inside. > > Alternatively, do you think I should switch to spheres representation? > But I still would need to blur the spheres to achieve the low-resolution > look of the domain. I am presuming that by "low resolution" you mean that you have increased the solvent radius from the default of 1.4 to something larger, like 6 Angstroms. I see that this can result in gaps in the surface. I wouldn't call it clipped, though. If you draw a solvent accessible surface instead of a molecular surface (by setting the variable surface_solvent to 1 instead of 0) then the gaps will disappear, but the surface will now be 6 Angstroms out from the van der Waals surface. It doesn't appear to have gaps now. Alternatively, you can draw the surface using the MSMS program. It does not have the same artifacts as the built-in PyMOL surface generation routine for large probe radii. I have a script for running that from within PyMOL: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/msms_pymol.py Unfortunately I have not written any colouring schemes to the script other than specifying a single solid colour for the whole surface (or two colours if you specify a selection, e.g. if looking at an interface surface). Hope this helps, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
