RE: [PyMOL] labeling atoms in GUI

2003-10-31 Thread Warren L. DeLano
Richard, It's not GUI, but you could simply bind a function key such as F1 to that command: cmd.set_key('F1',lambda :cmd.label("(lb)",'"%s %s %s"%(name,resn,resi)')) You might then want to bind 'F2' to something which hides all labels. cmd.set_key('F2',cmd.label) Cheers, Warren -- mailto:war.

RE: [PyMOL] secondary structure assignment and surface potential calc/mapping

2003-10-31 Thread Warren L. DeLano
> 1) Is the secondary structure assignment function in 0.92 > more reliable? Or does the "WARNING: it will make mistakes, > so don't publish anything based on this algorithm!" statement > still apply? Good question! I added that warning message to "util.ss" back when I believed that there was

[PyMOL] secondary structure assignment and surface potential calc/mapping

2003-10-31 Thread Neiditch, Matthew
Dear List, 1) Is the secondary structure assignment function in 0.92 more reliable? Or does the "WARNING: it will make mistakes, so don't publish anything based on this algorithm!" statement still apply? 2) Is there a 0.92 function to calculate and map surface potential? This would be useful be

[PyMOL] a couple of newbie questions

2003-10-31 Thread Andrew Fant
Hello all. I am relatively new to pymol, so please excuse me if these questions are too simple for the list as a whole. I am running 0.90 on a Linux system by way of introduction. 1) What is the easiest way to select one molecule out of several on the screen and translate it independentl

RE: [PyMOL] secondary structure and movie

2003-10-31 Thread Warren L. DeLano
Alan, Unfortunately, secondary structure is currently defined as an atom rather than a coordinate property. Thus, in order to "animate" secondary structure, you'll need to run dss automatically for each state. For example: mset 1 -5 mdo 1, dss state=1 mdo 2, dss state=2 mdo 3, dss state

[PyMOL] secondary structure and movie

2003-10-31 Thread Alan Wilter Sousa da Silva
Hi List! I did a polyalanine in helix ss. I tested: 1: dss (ok) 2: run stride_ss.py, stride2pymol (ok) 3: dssp (from rtools) (???) Case (1) differs a little bit from (2) in N term. Case (3) seems not to work. Or, maybe, I do not know how to use it. Tried via menu and via command dssp. Got the s