Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Rolf Huehne
On 08/20/2013 01:18 AM, Robert Hanson wrote: Sure. rotate BEST does more than simple 90-degree rotations. Could be different definitions of what is best of course. What it has now is smallest volume with thinnest side directed toward the user and longest side along X. Were you sure to

Re: [Jmol-users] reordering IRC frames and pasting two halves together

2013-08-20 Thread Whitwell, George
It now reads the energy of the first model, but only the positions for the rest. Readers of this conversation should note the typo in the getProperty below: should be- print getProperty(modelInfo.models[1].energy) From: Robert Hanson [hans...@stolaf.edu]

[Jmol-users] Reversing IRC files

2013-08-20 Thread Greeves, Nick
I use MacMolplt to stitch together GAMESS/ Firefly IRC output files. When you add extra frames there is a check box to reverse the order. We have used this for all the animations on chemtube3d.com All the best Nick Sent from my iPad 2 On 20 Aug 2013, at 05:25,

Re: [Jmol-users] reordering IRC frames and pasting two halves together

2013-08-20 Thread Robert Hanson
That's probably because I don't have any IRC output from GAMESS. If you send one to hans...@stolaf.edu, I can fix that. On Tue, Aug 20, 2013 at 7:13 AM, Whitwell, George gwhitw...@ncwc.eduwrote: It now reads the energy of the first model, but only the positions for the rest. Readers of

Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Robert Hanson
Hmm. Shouldn't work that way. ROTATE BEST initializes with a restore orientation (or, at least it effectively does that, because it multiplies in the inverse of the current rotation quaternion). What was the exact sequence of commands you used there? As far as I know, the only way it can give a

Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Rolf Huehne
On 08/20/2013 04:20 PM, Robert Hanson wrote: Hmm. Shouldn't work that way. ROTATE BEST initializes with a restore orientation (or, at least it effectively does that, because it multiplies in the inverse of the current rotation quaternion). What was the exact sequence of commands you used

Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Robert Hanson
Rolf, console problem -- yes, I saw that on a Mac last weekend. I'll look into it. Something about the way the mouse events are being handled in Safari, I think. Can you try Firefox or Very frustrating! rotate: sorry, I can't reproduce that, hard as I try. Rotate BEST executes this: q

Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Rolf Huehne
On 08/20/2013 06:43 PM, Robert Hanson wrote: Rolf, console problem -- yes, I saw that on a Mac last weekend. I'll look into it. Something about the way the mouse events are being handled in Safari, I think. Can you try Firefox or Very frustrating! I am not using Safari. I am using Firefox

Re: [Jmol-users] new Jmol feature: rotate BEST

2013-08-20 Thread Robert Hanson
I found it. A bug in the new JSmoljQueryExt.js that allows JSmol now to be used with user-provided jQuery if desired. See http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20b.zip I think that fixes the mouse problem -- or at least it should get rid of that stream of messages coming from

Re: [Jmol-users] reordering IRC frames and pasting two halves together

2013-08-20 Thread Robert Hanson
http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20b.zip -- Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and

[Jmol-users] JSmol hacks to jQuery removed

2013-08-20 Thread Robert Hanson
JSmol users, With recent improvements to jQuery, I'm happy to announce that there is no longer any need for any custom jQuery version for JSmol (JSmoljQuery.js). A new file, JSmoljQueryExt.js extends jQuery to allow synchronous binary file loading, MSIE cross-domain AJAX, and the popup menu and

[Jmol-users] Bonding in cif files

2013-08-20 Thread Tom Daff
Hi, I have two questions regarding the reading of bonding in cif files. I would like to load a cif file and use both the unit cell information and the bonding information from the GEOM_BOND, but I have tried several combinations of options, and can only seem to get the autobonding when the unit

Re: [Jmol-users] Need help with protein residue protonation states and assign atom ({}) Pl/Mi command (JSmol)

2013-08-20 Thread Vinushka Schalk
After a big network upgrade and installing the latest version (the one that eliminated the need for JSmoljQuery), everything seems to be working fine. I have tried various protonation and deprotonations on all of my test cases and they all seem to produce no further issues. Thank you very much!

Re: [Jmol-users] Need help with protein residue protonation states and assign atom ({}) Pl/Mi command (JSmol)

2013-08-20 Thread Robert Hanson
super! Glad to have been a help. Do point us to it when you feel that is appropriate. -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer

Re: [Jmol-users] Bonding in cif files

2013-08-20 Thread Robert Hanson
Easy question first: _ccdc_geom_bond_type should not be a big problem. I do see what you are talking about. For example: http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt has A for aromatic. That is no problem. A preliminary attempt is at