[PyMOL] Plugins

Hi We are looking at possibly writing some plugins to extend the functionality of PyMOL. How would we go about this? Is there some documentation on the general process? Any help would be greatly appreciated!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit University of Pret

[PyMOL] launching PyMol from a python function

I'm trying to start PyMol from another python program. After the 0_99beta17 it is possible to start it from the __main__ part of a code. But when I start PyMol from a function 'pymol.finish_launching()' goes in an endless loop. Here goes an example: ---

[PyMOL] rTools

Another rTools question! With the following script I get png files written for frames 1-11 and for 22-33, but none for the morphing part of the script. In fact, I cannot get any output images when running mv_morph in any context, either alone or with other commands. But the images displayed in

Re: [PyMOL] question about ray after alter and rebuild

Hi Pete, Check on the sections "clipped_by" and "bounded_by" in the povray documentation. You can clip with a defined plane, and can actually do so using different planes for different objects. Alternatively you can use other objects to clip. Another possibility is to use CSG difference or interse

Re: [PyMOL] question about ray after alter and rebuild

> Or you can dump to povray and render at whatever resolution you want, > but the image will not resemble exactly what is seen in the pymol viewer > window. > I've noticed problems with the clipping planes (z axis) whenever I've tried this. Specifically, the near clipping plane is apparently not

Re: [PyMOL] non-pdb coordinate help

Hi Kristl, The pdb-file is column formatted. You can find a specification of the file format at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html The easiest is to write a python script to do the conversion. Hope it helps, Tsjerk On 10/24/05, Kristl Adams wrote: > > I have se

Re: [PyMOL] question about ray after alter and rebuild

Or you can dump to povray and render at whatever resolution you want, but the image will not resemble exactly what is seen in the pymol viewer window. Peter Adrian Meyer wrote: >>multiple structura alignment. I pointed out three structures for further >>processing within all 12 structures. However

[PyMOL] non-pdb coordinate help

I have several txt files of coordinates (mostly heme type compounds) that I'd like to format correctly for pymol to be able to read. I've tried several things looking at PDBs with hemes, but can't figure it out. Will someone with more experience please show me how this should be formatted for

Re: [PyMOL] Adjust radius of sphere

Hi Anbang Li, If you want to show the spheres in a relative size, you can use set sphere_scale, 0.5 to scale down the size by half for example. To do this for a specific object, use set sphere_scale, 0.5, object Otherwise, if you want to change the actual radius, you can use alter selection,

Re: [PyMOL] question about ray after alter and rebuild

> multiple structura alignment. I pointed out three structures for further > processing within all 12 structures. However, when I try to ray the > structural > resolution (only 3 of all 12 structures) to 2000x2000 with 'ray 2000, > 2000', I > always received a low resolution (as screen resolution o

[PyMOL] Adjust radius of sphere

Hi all, I have a question about radius of sphere: I select a atom, show its sphere, then I want to increase the radius of sphere. How to do this? Thanks for answers. Anbang Li