## [PyMOL] surface with vdw > 6

 [PyMOL] surface with vdw > 6 From: co1 - 2005-06-06 10:26:04 ```Hello, I would like to represent the surface of a model made of dummy C atoms, b= ut they should have a van der Waals diameter bigger than 6 A. When I increase their vdw above = 5.9 (for ex.: alter elem c, vdw=3D6; rebuild), the surface just disappear. Do I need to change some other parameters? Is it -actually- impossible for pymol to calculate a surface for a vdw > = 6A? I would appreciate any help and advice. Best regards. LC =0A=0AAcc=E9dez au courrier =E9lectronique de La Poste : http://www.laposte.net = ; =0A3615 LAPOSTENET (0,34=80/mn) ; t=E9l : 08 92 68 13 50 (0,34=80/mn)=0A= =0A ```

 [PyMOL] surface with vdw > 6 From: co1 - 2005-06-06 10:26:04 ```Hello, I would like to represent the surface of a model made of dummy C atoms, b= ut they should have a van der Waals diameter bigger than 6 A. When I increase their vdw above = 5.9 (for ex.: alter elem c, vdw=3D6; rebuild), the surface just disappear. Do I need to change some other parameters? Is it -actually- impossible for pymol to calculate a surface for a vdw > = 6A? I would appreciate any help and advice. Best regards. LC =0A=0AAcc=E9dez au courrier =E9lectronique de La Poste : http://www.laposte.net = ; =0A3615 LAPOSTENET (0,34=80/mn) ; t=E9l : 08 92 68 13 50 (0,34=80/mn)=0A= =0A ```
 RE: [PyMOL] surface with vdw > 6 From: Warren DeLano - 2005-06-06 21:35:39 ```LC, PyMOL's surfacing algorithm current only works well for standard atomic = geometries...radii in the 1 - 3 A range, and solvent radii of 1-3 A. = Perhaps you can simply scale the problem to fit within that range? 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:warren@... =20 =20 > -----Original Message----- > From: pymol-users-admin@...=20 > [mailto:pymol-users-admin@...] On Behalf Of co1 > Sent: Monday, June 06, 2005 3:26 AM > To: pymol-users > Subject: [PyMOL] surface with vdw > 6 >=20 >=20 > Hello, > I would like to represent the surface of a model made of=20 > dummy C atoms, but they should have a van der Waals diameter=20 > bigger than 6 A. When I increase their vdw above 5.9 (for=20 > ex.: alter elem c, vdw=3D6; rebuild), the surface just disappear. =20 >=20 > Do I need to change some other parameters?=20 > Is it -actually- impossible for pymol to calculate a surface=20 > for a vdw > 6A? >=20 > I would appreciate any help and advice. > Best regards. > LC >=20 >=20 > Acc=C3=A9dez au courrier =C3=A9lectronique de La Poste : = http://www.laposte.net ; > 3615 LAPOSTENET (0,34=E2=82=AC/mn) ; t=C3=A9l : 08 92 68 13 50 = (0,34=E2=82=AC/mn) >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by: NEC IT Guy Games. How far=20 > can you shotput > a projector? How fast can you ride your desk chair down the=20 > office luge track? > If you want to score the big prize, get to know the little guy. =20 > Play to win an NEC 61" plasma display: http://www.necitguy.com/?r=20 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 ```