Pietro, Below is an example script demonstrating how to create low-resolution structure "blobs" using PyMOL:
load $TUT/1hpv.pdb, inp remove not polymer alter all, b=50 alter all, q=1 set gaussian_resolution,4 map_new mapA, gaussian, 1, inp and chain A, 6 isosurface surfA, mapA set gaussian_resolution, 8 map_new mapB, gaussian, 2, inp and chain B, 10 isosurface surfB, mapB color wheat, surfA color teal, surfB Note that the temperature factor field (b) has at least as much impact as the resolution setting, so in practice, increasing b factors is the more computationally efficient way of increasing the blur effect. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Pietro Roversi Sent: Thursday, September 11, 2008 5:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] I want to represent a domain of my molecule as a lowresolution solid shape Dear everyone, I want to represent a domain of my molecule as a low resolution solid shape. I have chosen surface representation but the surface is clipped, exposing the inner part, which makes the domain appear hollow. The rendering of the inner surface appears greyish and different from the outer part. Can I make the clipped surface filled so that this greyish inner part is not there anymore? It should look solid inside. Alternatively, do you think I should switch to spheres representation? But I still would need to blur the spheres to achieve the low-resolution look of the domain. Thanks for any suggestions you can provide! Regards Pietro -- Pietro Roversi Sir William Dunn School of Pathology, Oxford University South Parks Road, Oxford OX1 3RE, England UK Tel. 0044-1865-275385 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
