for smoothen rendering, you can use the "smooth", "set ribbon_smooth"... commands or try to raytrace your molecule thanks to the "ray" command.
Concerning transparency, there is no simple way to my knowledge to render transparency on some of the residues of a single loaded protein. You could trick with loading modified PDBs with and without the desired residues then apply the transparency on only one but in some cases I guess it can modify the geometry.
On the other hand, you can absolutely apply transparency to a molecule and not another one ("set transparency=0.5") or to a secondary structure and not another one (eg : sticks transparent and not ribbons, "set stick_transparency=0.5")
Hope this will help
Virgile
At 03:35 PM 3/16/05 +0000, Paula Salgado wrote:
Hi,
I'm a new pymol user and have been trying to generate an image
of a solvent-accessible surface in pymol. How can I smooth the
surface representation?
Another questions relates to transparency: is it possible to
have bits of a protein transparent and others coloured? If so,
how can you do it? and for 2 different proteins, can you get
one transparent and not the other?
Thanks for your help!
Paula
Paula Salgado
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive
Headington
Oxford
OX3 7BN
UK
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Virgile Adam (office 14.1.07 - Sector 14)
European Synchrotron Radiation Facility (ESRF)
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Mail : virgile.a...@esrf.fr - Tel : 04 76 88 24 57
***Sometimes I think the surest sign that intelligent life exists elsewhere in the universe is that none of it has tried to contact us***
European Synchrotron Radiation Facility (ESRF)
6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 9 France
Mail : virgile.a...@esrf.fr - Tel : 04 76 88 24 57
***Sometimes I think the surest sign that intelligent life exists elsewhere in the universe is that none of it has tried to contact us***
