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RE: : [PyMOL] Surface Vertex Coordinates
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From: Warren D. <wa...@de...> - 2006-03-17 06:53:21
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> Of course it would be a whole lot easier if PyMol output VRML=20 > directly =20 > ..... Warren ????? Chris Want's latest VRML2 code is now in CVS (with a few minor tweaks of my own...) save my_vrml.wrl Cheers, Warren -- Warren L. DeLano, Ph.D. =20 Principal Scientist . DeLano Scientific LLC =20 . 400 Oyster Point Blvd., Suite 213 =20 . South San Francisco, CA 94080 USA =20 . Biz:(650)-872-0942 Tech:(650)-872-0834 =20 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:wa...@de... =20 =20 > -----Original Message----- > From: pym...@li...=20 > [mailto:pym...@li...] On Behalf Of=20 > Laurence Pearl > Sent: Wednesday, March 15, 2006 9:35 AM > To: Benjamin Hitz > Cc: pym...@li... > Subject: Re: : [PyMOL] Surface Vertex Coordinates=20 >=20 > The Povray intermediate file generated when you do 'ray=20 > renderer =3D 1' =20 > contains all vertices, normals and colouring information for=20 > cartoon and surface object types. However you do need to=20 > produce a parsing script to extract these in to a useful form=20 > for importing into other programs. Have a look at the front=20 > cover of Mol Cell vol 20(4) - I generated a cartoon of the=20 > protein in PyMol, output it as a povray file, and then=20 > converted it to VRML using a jiffy produced by Chris =20 > Richardson, and then used it as an object in the Blender 3D=20 > modelling =20 > package to generate the picture. >=20 > Of course it would be a whole lot easier if PyMol output VRML=20 > directly =20 > ..... Warren ????? >=20 > Laurence Pearl >=20 >=20 > On 15 Mar 2006, at 17:01, Benjamin Hitz wrote: >=20 > >> > >> I am interested in the coordinates of the vertices of the mesh=20 > >> representation of the molecular surface. Is there any=20 > method to read=20 > >> them out? > >> > >> Thanks > >> > > > > Me too. With coloring and/or other "property" information as well. > > > > > > > > -- > > Ben Hitz > > Senior Scientific Programmer ** Saccharomyces Genome Database ** GO=20 > > Consortium Stanford University ** hi...@ge... > > > > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by xPML, a groundbreaking scripting=20 > > language that extends applications into web and mobile=20 > media. Attend=20 > > the live webcast and join the prime developer group=20 > breaking into this=20 > > new coding territory! > > http://sel.as-us.falkag.net/sel?=20 > > cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D121642 > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > -------------------------------------------------------------- > ---------- > -- > Laurence H. Pearl >=20 > Section of Structural Biology, Institute of Cancer Research > Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK >=20 > Phone +44-(0)20 7153 5422 : Secretary +44-(0)20 7153 5443 > FAX +44-(0)20 7153 5457 : E-Mail Lau...@ic... > -------------------------------------------------------------- > ---------- > -- > " Live Simply and do Serious Things .. " - Dorothy Crowfoot Hodgkin > -------------------------------------------------------------- > ---------- > -- >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking=20 > scripting language that extends applications into web and=20 > mobile media. Attend the live webcast and join the prime=20 > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720& > dat=3D121642 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 >=20 >=20 >=20 |