[PyMOL] ca-trace

Hidy Pymollers I *think* I've RTFMed everywhere I can, but I haven't been able to figure out how to draw a molecule C-alpha only. When I selected all CA atoms, I got a cloud of dots that were not connected. I suspect I've missed something fundamental... Thanks for any tips Phraenquex

RE: [PyMOL] pymol sys.argv, winnt, barks

Andrey, I deduce you're referring to windows? I think this is what you get when python gets installed in C:\Program Files\python or some other location that is not on the (hardcoded?) search path of pymol, which means it can't find the tcltk libraries. The solution is to install python on C:\pyt

RE: [PyMOL] Learning Python for PyMOL

vim (Improved Vi editor) which is on RedHat and probably most other Linux, also is python-sensitive. It does pretty colours and stuff, so for all you vi loyalists, there's no need to go over to the Dark Side. :) phx. > -Original Message- > From: DeLano, Warren [mailto:war...@sunesis.com]

RE: [PyMOL] ccp4 map?

I believe pymol reads ccp4 maps... at least, it did a few months ago :) To do the conversion off-line, you'd have to install ccp4, then you could use something like xdlmapman. phx. > -Original Message- > From: Ben Cornett [mailto:acor...@emory.edu] > Sent: Wednesday, March 20, 2002 1

RE: [PyMOL] HOWTOS

Very interested - and if it's been started, others (such as me) will have a formal place to make contributions. (Or is something already set up???). phx. > -Original Message- > From: Eric Ross [mailto:e...@biochem.utah.edu] > Sent: Thursday, May 09, 2002 12:55 PM > To: pymol-users@li

RE: [PyMOL] Continuous surfaces?

Hi Peter What happens is that the surface is CREATED for the whole object, but only DISPLAYED for the selection. You have to make a new object, and then draw the surface of that: create newobject, (chain a AND i;49-63) show surface, newobject Cheers phraenquex > -Original Message- > Fr

RE: [PyMOL] Polypeptide conformation restriction

Hi Liang: The most up-to-date contour on the Ramachandran plot you can find at the molprobity website: http://kinemage.biochem.duke.edu/molprobity/ It's a bit indirect, you have to submit a structure and then it will give back a Ramachandran plot - but this plot agrees pretty well with what we t

[PyMOL] Thoughts

Hi Warren Really great program already, and great promise. Here are some suggestions you may or may not like to know about; ideally, I'd have liked to give some code, but until I have bandwidth, I pass on the ideas. Seem to be fairly intrinsic things that may need some mulling over. 1) There'

RE: [PyMOL] Question about crystallographic symmetry

Hi Michael You seem to be after the biological assembly; in theory, pdb files from the PDB are supposed to have the matrix that will generate this somewhere in the header (REMARKS lines), and that shouldn't be too hard to parse out and apply explicitly to the molecule. Of course, pdb files are n