Re: [PyMOL] label transparency

2009-03-10 Thread Warren DeLano
Neil, Unfortunately, transparency is not supported for labels (at present). Cheers, Warren From: Neil Ranson [mailto:n.a.ran...@leeds.ac.uk] Sent: Tuesday, March 10, 2009 8:31 AM To: pymol-users@lists.sourceforge.net Subject: [

Re: [PyMOL] Trying to get rms and rms_cur to run

2009-03-10 Thread Warren DeLano
Evan, Normally, fit, rms, and rms_cur require that all atom identifiers match. However, we're trying to increase flexibility by supporting alternate pairwise "matchmakers"...assuming (A) that you're running 1.2 beta 3 and (B) that the atom names match: rms_cur m1, m2, matchmaker=4 may work.

[PyMOL] label transparency

2009-03-10 Thread Neil Ranson
Dear All, Does anyone now if it's possible to alter the transparency level of a label? I have an object that is scripted to fade in and out, and I would like to bring the labels in and out at the same speed, but can't seem to find a setting that works. Thanks in advance, Neil. Neil Ranso

[PyMOL] Trying to get rms and rms_cur to run

2009-03-10 Thread Evan Kantrowitz
Hi Folks, I have two positions of one small molecule. I am trying to determine the RMSD between them without doing an align I read the molecules into pymol as m1 and m2. As seen below each has 23 atoms. When I do an rms it gives the error: No atoms selected, but if I do an align it