RE: [PyMOL] polar contact definition

Sergio, We use the term "polar contacts" because, as you correctly point out, some of the contacts shown don't meet strict hydrogen-bonding criteria. Of course, many macromolecular crystal structures aren't of high enough resolution to make definitive determinations anyway...so... With ideal geo

[PyMOL] polar contact definition

Dear Pymol users: I'm using pymol to find "polar contacts". I'm wondering what is the definition of a "polar contact". Some of the distances are longer than expected for a hydrogen bond. So, I'm left wondering what is the distance cut off employed. Thanks -Sergio

[PyMOL] distance between aromatic residues

Hi List, I was wondering if anyone knew of a way to set a distance measurment between two aromatic rings, where the distance is measured from the center of the ring, rather than a specific atom. thanks Sara Nichols

RE: [PyMOL] Pymol colors and selections

Andrew, Here's how I would write that script: load PDBs/prot.pdb, prot bg_color white util.ray_shadows('light') set cartoon_fancy_helices, 1 hide everything, prot select Cterm, A/200-300/ show cartoon, Cterm set cartoon_color, green show surface, Cterm set transparency, 0.3 set surface_color,

RE: [PyMOL] delete object states

Martin, Unfortunately this doesn't exist yet, but I agree that it is a necessary function. The best you can do right now is load a blank PDB file into that state. That should delete the coordinates for that state, but it doesn't actually delete the state. # to delete the coordinates for state 2

[PyMOL] Pymol colors and selections

I'm having PYMOL trouble with something that should be easy: I want to make a green ribbon diagram, a grey transparent surface, and then display residue side chains in red underneath. I'm having trouble with selections that set up these three items as discrete things I can color as I choose.

Re: [PyMOL] Slow transparency

It was just me - loading a .pse created with the previous version seemed to be the problem. When I loaded a new coordinate file into that session, everything seemed to click back to normal. On 23 May 2005, at 12:56, Laurence Pearl wrote: Is it just me or has the new release of MacPyMol gone

[PyMOL] Built-in movie commands

Could someone please point me to a description of built-in PyMol movie command (movie.roll, movie.zoom, etc.). I was able to use them but I have a strong feeling that they can do more then I was able to guess. Thanks in advance, Jendrek > A designer knows he has achieved perfection > not

[PyMOL] Slow transparency

Is it just me or has the new release of MacPyMol gone very slow when rendering transparent surfaces ? -- Laurence H. Pearl Section of Structural Biology, Institute of Cancer Research Chester Beatty Laboratories,

[PyMOL] delete object states

Hi PyMOLers! I've searched the documentation, wiki, and this mailing list for a way to delete particular states of an object, but have found nothing. Is this feature not implemented or am I just poor at searching? I think it is quite an essential feature when viewing trajectories from molecula

[PyMOL] display variables

dear list, is it possible to distribute the pymol gui and the viewer between different display variables, say the gui to "display:0.0" and the viewer to "display:0.1"? regards, marc bruning