======================================================================
Changes made:

Commented jtatdemo/ch_view2/view02.spt to indicate how the surface can
be generated.
======================================================================
Problems (see also below):

Need to document that when the molecule changes, spinningStart does not work;
should use spinningOn instead? (Did in Chapter 6 of MHC.)

After checking center, then clicking entire molecule, next click centers atom.

Centering all should be center visible, but can that be done slowly?

(not marked: bug: after using center checkbox, all echos have white bkg!)

======================================================================
Problems with Jmol 12.0.8:
1. Spin toggle failed because newly exit stops spinning. Bob promises to
change this. Workaround (in dualquad.js) use "!show spin;" instead of
"exit; show spin;".

2. In chapter 2 (subtitles, flu neuraminidase), the isomesh color
is magenta instead of yellow, the pocket is more extensive, seeming
to include cavities in addition to pockets.

3. There appears to be a bug in the side by side chapter in both versions
of Jmol. When you click View 2, the top 2 have antialiasing off and spin
fast, while the bottom one has it on and spins slowly. Returning to view 1
sometimes has both with antialiasing off and fast spinning. (Is there a command
in the script that is generating and error and killing it?) Similar problems
occur in views 3, 4, and 5 (antialiasing tends to be off at the start).

4. Check "center clicked", then "click here to center all". Centering is
above center.

5. Distance line sticks to edge of Jmol, disappears on next click inside.

6. After the final double click fixing a dihedral, a pink line follows the
mouse. This does not happen on distances or simple angles.

Changes in (next) version:
  	Release: polling? noSpinning (config2.js)
  Bug fix: included css4all/tutorial.css in contents.htm
  chapter/jcontrol.js for checkboxes appears to have been in 9/8/08??
	Added set (lighting) and "set defaultVDW rasmol" to jtat/_sptutil/vreset.spt.

Changes in September 8, 2008 version (Version 1.0, first official release).
	New chapter on colors.
	Completed Authoring Instructions.
	Center all implemented.
	Checkboxes implemented, jcontrol.
	Improved list of links to PDB files for further exploration, now
		permitting, for online tutorials, FGiJ links to PDB files not
		available from RCSB.


Changes in July 12, 2008 version:
	New chapter on animations and movies.

	Included proteopedia in linx per pdb code.
	Details in Contents above (for intro) as well as below chapters.

======================================================================
Need to correct the error about file sizes for movies vs. animations.
The large multi gif is 0.5 megs, not 5 megs!
======================================================================
RELEASE

Delete _sptutil/cs_*.spt (used only in f1-atpase and mhc).

Restore spinning!

--------------------
FUNCTION

Center all on white bkg?!

bug: spinningSame does not work when the molecule changes.

/find a better movie?

Enable polling?

--------------------

DOCS TODO

	removed one blank line between view buttons.
	if you want more space, put <br> or <br><br> in iPreButtonText.

tell symptom when forget to comment out load in state script.

color keys for temperature?

Retool anims & movies a la notes from Frieda? (Did a lot of revision
already.)

Suppress now showing view message in Animations and Movies, and document
how there.

---------------

Calling jmolCheckbox() in a button description causes Jmol to fail to load.
Calling it to return the html inline does the same.
Tried calling it onLoad and putting output into a division, in ch_drums.

======================================================================
For "center all" button, see jmol-users emails of 4/13/07 "button experiments"
and demo
http://chemapps.stolaf.edu/jmol/docs/examples-11/buttons.htm
and under "set echo", the ability to use an image as the echo (e.g. a button
image!).
See the elegant and illustrious scripts linked to Bob's email

TAKE OUT THE academics/chemapps/
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/data/btnSurface.spt
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/data/btnAnim.spt
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/data/btnCavity.spt

NB in Manual
set echo user-named IMAGE "file name"
======================================================================

set measurements angstroms
zoomlarge = false;
defaultdirectory = "data"
load lac_dna1.pdb.gz;
moveto /* time, axisAngle */ 1.0 { -90 -593 801 174.6} /* zoom, translation */  200.0 -0.08 -15.6  /* center, rotationRadius */ {-0.7555008 -5.6904993 -2.0655003} 48.285587;

select *:A;color purple;
select *:B;color green;
color ssbonds [255,200,50];
anim fps 10; anim mode palindrome;

btnSetup=true

	script btnSurface.spt
	script btnAnim.spt
	script btnCavity.spt
	script btnCartoon.spt

btnSetup=false

set echo all;font echo 15
======================================================================
Note that btnCartoonbg is a different echo name that btnCartoon.
The bg has the script assigned to it.

if (btnsetup)
	set hoverdelay 0.1 <<<<<<<<<<<<<<<<
	set echo btnCartoonbg 70% 0%
	set echo btnCartoonbg center <<<<<<<<<<<<<<<<
	echo "                         "
	color echo background translucent 0.8 yellow
	set echo btnCartoonbg script "script btnCartoon.spt" <<<<<<<<<<<<<<<<
	set echo btnCartoon 70% 0%
	set echo btnCartoon center
	color echo background translucent 1.0 yellow
	cartoonOn = true
endif

set echo btnCartoon <<<<<<<<<<<<<<<< FOR ECHO COMMANDS BELOW
cartoonOn = !cartoonOn


if (!cartoonOn)
	select all
	cartoons off
	select nucleic;
	spacefill;
	select protein;
	wireframe 0.2;
	ssbonds 0.25;
	echo cartoons <<<<<<<<<<<<<<<<
	color echo green
else
	restrict none;select all
	cartoons on
	echo spacefill <<<<<<<<<<<<<<<<
	color echo red
endif

----------------------------------------------------------------------

Why is HETATM APC deemed to be RNA instead of ligand in both 1.02 and 1.39?

Can't disablePolling in Safari with version online, in F1-ATPases.
DISABLED POLLING AND RED MESSAGE FOR VERSION july 12 2008.

Show the bottom and top details for contents in the jtatdemo.

In the instructions for updates, I forgot to tell people to copy the *4all
directories from template to their new tutorial directory.

Google analytics instead of sitemeter?

Put an empty author.css file in _cssutil for people to add their own
all-tutorial styles?

Among shells, mention
Tim Herman/Rockefeller/RNA Polymerase Holoenzyme tutoiral.
Also Mitchell Guss <M.Guss@mmb.usyd.edu.au>
"Dr. Howard M. Einspahr" <online.submission.f@iucr.org>
Einspahr, H., and Guss, M. 2008. A new service for preparing
enhanced figures in IUCr journals. Acta Crystallographica Section
F64: 154-155.

And get Herman's high school students into molvisindex!
www.pingrysmartteam.com/RPo/RPo_body.htm

Add Angel's snapshot code.

Put sussman movie sent by Karl O in Demo Tut.

set antialiasdisplay/translucent checkbox

add # Begin Script for Initial View / # End Script for View 6

straighten out the drums scripts file location

show errors in Jmol console in red? (since can't easily search for them)

auto insert # exiting from vreset.spt in set debugscript stream? It is the only inline all-command reporting mechanism. set historylevel reports the commands within a .spt file out of sequence and not delimited with .spt filename labels.

Echo number of script errors in center of Jmol in red "5 command
script errors!"?

Otherwise when errors don't make obvious unexpected results in
the molecular view, you may not realize they are occurring.
--------------------
TO DO

allow synch when spinning?

remove table1.css from _cssutil.

remove colors.js from js4all in jtatdemo.

enable 2hu4 in jtatdemo (advanced) to come from PQS.

-----------------
Later?
jump to any view?

Have replay/reset buttons use reset.spt instead of initial-view.spt?

==========

credit angel with solution for centering, resizabl, ...?
frieda! Tim! Bob!

echo font size conditional on jmol size?

revise color control mech comment at top of util.js

================================================================

Include jmol.jar APPLICATION for script development (to save downloading
it).

try a URL in molecules.js

add standard color keys? see keys.js

------------
2/3/4-Jmol comparison support
	see _jsutil/dualquad.js

------------------------
------------------------
RELEASE SEQUENCE
	Prepare the JTAT documentation!
	Prepare the tutuse doc.

	Release JTAT at bi.o/wiki!

	Clean up initial scripts js.

----------------------------
FILENAMES
script file names can be anything

Frieda says use dvrblite.js for googling so I can use recognizable filenames.
Indeed, googling that filename gets only gpons site! (Not even Tim's which was
only a zip file for download).

mhc/contents/contents.htm (mhc/index.htm for introduction text/refs)

mhc/js4all/title.js (was content.js)
mhc/js4all/molecules.js
mhc/js4all/license.js

mhc/molecules4all/*.pdb (all pdbs for this tutorial)
mhc/scripts4all/*.spt (common to >1 chapter)

Put contents and chapters in directories

	dir name: contents or chapter01 (later insertions: 015 or 01a)

		contents.htm or chapter.htm

		initial-view.spt  (was frontispiece.spt)
	
		view01.spt (later insertions: 015 or 01a)

		other chapter-specific spts (else they go in scripts4all)

