Re: [Jmol-users] Calculate structure results

Beta in parentheses may be ok. I was so focused on beta turns that I did not stop and consider what the presence of the parentheses would mean. Another issue with color is with hydrogen bonds of beta sheets. Presently these hydrogen bonds come in two colors. The colors document only shows one.

Re: [Jmol-users] Really Ugly Windows Firefox Issue

Angel- Thanks for the information. I'll try to update now. I don't think an update 3.6.15 was expected. I think the next update was supposed to be 4. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org --

Re: [Jmol-users] Really Ugly Windows Firefox Issue

I just got notice of the latest upgrade: What´s New in Firefox 3.6.15 Firefox 3.6.15 fixes the following issues found in previous versions of Firefox 3.6: * Fixed an issue where some Java applets would fail to load in Firefox 3.6.14 It works now! Two page reloads, no problem in the appl

Re: [Jmol-users] Calculate structure results

> OK, bad assumption on my part. I was assuming it was identifying beta turns. > The Colors document on the > Jmol site does indicate blue for beta turn. My fault. So we should say just "turns", right? Will do that Aha, that's why I put beta in parentheses last time! strand [255,200,0] FFC8

Re: [Jmol-users] Calculate structure results

OK, bad assumption on my part. I was assuming it was identifying beta turns. The Colors document on the Jmol site does indicate blue for beta turn. Karl >>> Robert Hanson 03/03/11 8:18 PM >>> Karl, Here's the report for 2mhr according to DSSP, which we are using now for Jmol's standard st

Re: [Jmol-users] Calculate structure results

Hi, Furthermore: On Fri, Mar 4, 2011 at 1:15 AM, Robert Hanson wrote: > T : A:65_A:66 An R-L nest that is part of a Schellmann loop > T : A:68_A:69 A type I beta-turn > T : A:86_A:86 A type I turn (also a niche3/4 bound to a water) > T : A:110_A:110 Hmmm. Not a turn. Looks like the helix from

Re: [Jmol-users] Help with surfaces

Hi Bob, Actually i didn't generate this .cos files, so i don't know if it was used the .mol file and , therefore, i don't know if they were supposed to match. But i think for my purpouse it would be easier to avoid creating a .jvxl file, since i can use the function loadCosmo and it works. I would

Re: [Jmol-users] Newbie question: showing a docked receptor-ligand model (applet)

Thank you very mucho for your help! > The difficulty is defining the atoms involved in the receptor...showing > bonds and ribbons in the entire protein is quite easy: > > select protein; cartoon on; > > The ligand will display initially as bonds and atoms. I suspect this isn't > what you want :-)