I tried the transparency to 0.5 suggestion and couldn't get to
work... may be I'm doing it wrong...
from the replies I got and looking at the options, I got the
impression you can only have transparency in 2 different
objects if they are represented in different ways - is taht
the case? what I was trying to do is create a figure for a
superposition of 2 molecules, having the non-superimposable
bits transparent in both and the superimposable ones colored -
is this possible in pymol? if so, how can i do it?
my surface now looks much nicer, thank you for your help!
---- Original message ----
>Date: Wed, 16 Mar 2005 20:17:31 +0100
>From: Virgile ADAM <virgile.a...@esrf.fr>
>Subject: Re: [PyMOL] surfaces and transparency
>To: pa...@strubi.ox.ac.uk, pymol-users@lists.sourceforge.net
>
> Dear Paula,
> 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)
> 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***
Paula Salgado
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive
Headington
Oxford
OX3 7BN
UK
