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Re: [PyMOL] surfaces and transparency
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From: Virgile A. <vir...@es...> - 2005-03-16 19:16:50
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<html> <body> Dear Paula,<br> for smoothen rendering, you can use the "smooth", "set ribbon_smooth"... commands or try to raytrace your molecule thanks to the "ray" command.<br> 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.<br> 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")<br><br> Hope this will help<br><br> Virgile<br><br> At 03:35 PM 3/16/05 +0000, Paula Salgado wrote:<br> <blockquote type=cite class=cite cite>Hi,<br><br> I'm a new pymol user and have been trying to generate an image<br> of a solvent-accessible surface in pymol. How can I smooth the<br> surface representation? <br><br> Another questions relates to transparency: is it possible to<br> have bits of a protein transparent and others coloured? If so,<br> how can you do it? and for 2 different proteins, can you get<br> one transparent and not the other?<br><br> Thanks for your help!<br><br> Paula<br> Paula Salgado<br><br> Division of Structural Biology<br> Wellcome Trust Centre for Human Genetics<br> University of Oxford<br> Roosevelt Drive<br> Headington<br> Oxford<br> OX3 7BN<br> UK<br><br> <br> -------------------------------------------------------<br> SF email is sponsored by - The IT Product Guide<br> Read honest & candid reviews on hundreds of IT Products from real users.<br> Discover which products truly live up to the hype. Start reading now.<br> <a href="http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click" eudora="autourl">http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click</a><br> _______________________________________________<br> PyMOL-users mailing list<br> PyM...@li...<br> <a href="https://lists.sourceforge.net/lists/listinfo/pymol-users" eudora="autourl">https://lists.sourceforge.net/lists/listinfo/pymol-users</a></blockquote> <x-sigsep><p></x-sigsep> <font color="#808080"><br> <div align="center">Virgile Adam (office 14.1.07 - Sector 14)<br> European Synchrotron Radiation Facility (ESRF)<br> 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex 9 France<br> Mail : vir...@es... - Tel : 04 76 88 24 57<br><br> ***Sometimes I think the surest sign that intelligent life exists elsewhere in the universe is that none of it has tried to contact us*** <br> </font></div> </body> </html> |