Re: [Jmol-users] Implementing custom commands

2012-03-21 Thread Adrià Cereto Massagué
El 21 de març de 2012 1:45, Robert Hanson hans...@stolaf.edu ha escrit: Custom commands can be simply set up by defining a function with that command name. is that what you mean -- sort of a macro? function colorMeBlue(atoms) { color @atoms blue } colorMeBlue {helix} Thank

Re: [Jmol-users] Question about rotation matrix

2012-03-21 Thread Nikolay Bogdanov
Thanks! Thus I do a proper rotation (which is my matrix multiplied by (-1) ) and then INVERTSELECTED, and that gives me what I want. Shouldn't this be a default action for the left-handed matrix rotation? Because now Jmol does something strange when one tries to apply a rotation/reflection

[Jmol-users] spartan file issue

2012-03-21 Thread Pshemak Maslak
Did anybody noticed problems with Jmol reading Spartan 10 .spartan files? I have observed that the current version of Spartan (10) produces files that cannot be read by Jmol. The error message reads: no atoms found. The file opens correctly in Spartan. The old version files produced by

Re: [Jmol-users] Question about rotation matrix

2012-03-21 Thread Robert Hanson
Well, that's an idea, anyway. How common do you think it is to have the actual matrix and not other information? On Wed, Mar 21, 2012 at 6:30 AM, Nikolay Bogdanov nikol.bogda...@gmail.comwrote: Thanks! Thus I do a proper rotation (which is my matrix multiplied by (-1) ) and then

Re: [Jmol-users] Implementing custom commands

2012-03-21 Thread Robert Hanson
That's Jmol script, not JavaScript. Yes, essentially exactly like pyMol. You can write any macro you want. 2012/3/21 Adrià Cereto Massagué adrian.cer...@urv.cat El 21 de març de 2012 1:45, Robert Hanson hans...@stolaf.edu ha escrit: Custom commands can be simply set up by defining a

Re: [Jmol-users] spartan file issue

2012-03-21 Thread Robert Hanson
Just send me a couple of files, Pshemak. On Wed, Mar 21, 2012 at 7:20 AM, Pshemak Maslak p...@chem.psu.edu wrote: Did anybody noticed problems with Jmol reading Spartan 10 .spartan files? I have observed that the current version of Spartan (10) produces files that cannot be read by

Re: [Jmol-users] Implementing custom commands

2012-03-21 Thread Adrià Cereto Massagué
El 21 de març de 2012 19:31, Robert Hanson hans...@stolaf.edu ha escrit: That's Jmol script, not JavaScript. Yes, essentially exactly like pyMol. You can write any macro you want. I didn't explain well. I can implement some of that functionality using JmolScript, but not everything I want. I

Re: [Jmol-users] Implementing custom commands

2012-03-21 Thread Robert Hanson
Ah, I see. Let's work on this. That's very interesting, and it's easy. Absolutely no hacking of Jmol code. It's all ready for you. A couple of options: 1) create a JmolScript function with the command name. That's your starting point. it doesn't matter what this function does. maybe