Re: [PyMOL] Saving the Connolly surface of a PDB

Jason Vertrees wrote: Hi Francios, Someone recently asked about this and the answer was that this should be a setting, but isn't currently available. If I have time, I'll try to sneak this in the upcoming PyMOL v1.4 release. Is there a workaround for the moment? For example, asking Pymol

[PyMOL] global illumination, volume representation and ipython

Hello, There's been quite a while since I wanted to ask this on the list, but would it be possible to have in Pymol some kind of technique to emulate realistic lighting (global illumination) in a rendered scene? The next point is related to the new volume representation. For example after

Re: [PyMOL] Saving the Connolly surface of a PDB

Hi Francois, That information is in the view matrix you get from get_view. The first nine numbers are the rotation matrix R. The next three numbers are the camera position c, followed by the three numbers denoting origin of rotation o. Then to transform your protein coordinates, as in the PDB, to

[PyMOL] Display coordinate vectors

Dear all I'm sure this question was answered before, but I could not find anything related to it in neither the mail list nor on the Wiki. Is it possible to display something like coordinate vectors in PyMOL? I.e. arrows in the 3d view space pointing towards [1,0,0], [0,1,0] and [0,0,1]? I

Re: [PyMOL] Display coordinate vectors

Hi, Martin, how about this: http://www.pymolwiki.org/index.php/Symmetry_Axis also check out the script drawing X, Y, and Z reference axes by Robert: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py hope it helps, hongbo On 04/08/2011 04:29 PM, Martin Hediger wrote: Dear all

Re: [PyMOL] Display coordinate vectors

great, thanks. On 08.04.11 16:42, Hongbo Zhu wrote: Hi, Martin, how about this: http://www.pymolwiki.org/index.php/Symmetry_Axis also check out the script drawing X, Y, and Z reference axes by Robert: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/axes_cyl.py hope it helps, hongbo

Re: [PyMOL] global illumination, volume representation and ipython

Hi Marius, There's been quite a while since I wanted to ask this on the list, but would it be possible to have in Pymol some kind of technique to emulate realistic lighting (global illumination) in a rendered scene? So, you're looking for something like ambient occlusion? If so, try this

[PyMOL] Convert pml script to Pymol Python script

Hi, I have a few pml scripts for pymol that I would like to rewrite properly in python, making use of Pymol's ability to interprete Python scripts. Do you know of an interpreter that converts pml scripts automatically to python scripts for Pymol? Since the number of tasks that you can do in pml

Re: [PyMOL] Convert pml script to Pymol Python script

Hi Matthias, There is no script that I'm aware of, but writing one should be rather straightforward because of how the API is organized: commandName arg1, arg2, arg3 becomes cmd.commandName(arg1, arg2, arg3) The hardest part would be determining when to quote strings versus not quoting

Re: [PyMOL] Convert pml script to Pymol Python script

It's not elegant at all, but it's worth knowing that you can use cmd.do(...) as a quick fix for lines that aren't immediately easy to convert. Even a mostly-working pml2py tool would be a useful addition to the wiki. Cheers, -Michael On Fri, Apr 8, 2011 at 2:09 PM, Jason Vertrees

Re: [PyMOL] global illumination, volume representation and ipython

Hello, On Fri, Apr 8, 2011 at 6:49 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Marius, There's been quite a while since I wanted to ask this on the list, but would it be possible to have in Pymol some kind of technique to emulate realistic lighting (global