Re: [PyMOL] Low resolution surface of large structures

Hi Yuxing, 3j3y has no b-factors (they are all 0.0), but the map_new command takes b-factors into account. The solution is, before calling map_new: PyMOL> set gaussian_b_floor, 50 Cheers, Thomas On 12 Feb 2015, at 16:12, Yuxing Liao wrote: > Hi all, > > I was trying to show low resolutio

[PyMOL] Low resolution surface of large structures

Hi all, I was trying to show low resolution surface representation for very large structures following the example at http://www.pymolwiki.org/index.php/Huge_surfaces. I was able to do it for the PDB 1AON using PyMOL>fetch 1aon, type=cif PyMOL>set gaussian_resolution, 10 PyMOL>map_new map, gau

Re: [PyMOL] shade on transparent spherical surface

Hi Jett, We are currently working on better (multi-level) transparency for all representations, this will be a feature for the next PyMOL release. In the current PyMOL version, you may see two artefacts for semi-transparent spheres in real-time rendering: 1) The "shading" that you describe com

[PyMOL] shade on transparent spherical surface

Hello, everyone, I've been trying use pymol to generate an image based on C-alpha coordinates only. I tried to set the sphere to be transparency by the command "set sphere_transparency, 0.5". However, the surface of the sphere shows some shading which looks quite odd. If I ray trace the image,