[PyMOL] Some plugin development questions

2010-03-04 Thread Michael Lerner
Hi all, I'm trying to pretty up the next version of the APBS plugin and I've run into two issues that I'm hoping others have solved: 1. Does anyone have any experience with PMW's OptionMenu? I've been trying something where I call an OptionMenu's setitem() and it keeps failing no matter what I

[PyMOL] disconnected loop in pymol

2010-03-04 Thread Anastassis Perrakis
Dear all, I have a small domain which is mostly loops, its a Cys-knot. All residues are in the preferred Rama regions, and all atoms are present in the PDB, but Pymol decides to 'break' my cartoon! Would anyone have a solution to force pymol draw a nice loop where the break is? (see small

Re: [PyMOL] disconnected loop in pymol

2010-03-04 Thread vincent Chaptal
Hi, I've seen this when using modeller and then working in coot to change parts of my model. The pdb looked like this: ATOM 2 CA ALA A 61 19.187 -16.491 60.818 1.00 7.01 AC ATOM 3 CB ALA A 61 17.667 -16.537 61.040 1.00 7.01 AC ATOM 4 C ALA A 61

Re: [PyMOL] disconnected loop in pymol

2010-03-04 Thread Eric Larson
Hi Tassos, Perhaps your pdb file has something in the segid column? For some reason Pymol cannot draw a connected cartoon if you values in the segid column so simply remove them. hope that solves your problem, Eric __ Eric Larson, PhD MSGPP Consortium Department of