> I'm almost done (I think) with script documentation. Take a look at
>
> http://www.stolaf.edu/people/hansonr/jmol/docs
* remove '@' from define ... it is for internal use only and will probably
change.
* color should list a few examples of coloring labels, cartoons, trace, etc.
* in the 'cpk' command we should tell people who CPK are
* dots should say 'vanderwaals surface or Solvent Accessible Surface. It
is closely related to 'set solvent on'/'set solvent {radius}'
* echo should say that it also echos to the console
* commands like 'font' that do not exist in RasMol/Chime should receive
some type of attention.
* Do all those options actually work for 'frame'?
* Hover should explictly say that it uses the label formatting escape
characters
* label should have a table of the %characters -> meaning
* refresh should be marked as deprecated. If someone is using it to
repaint the screen then they are asking for timing problems on other
machines. I cannot think of a good reason to use refresh. Presumably the
only time you want to refresh the screen is when you want the user to see
something. In which case one should use delay. The screen is automatically
refreshed when there is a delay command.
> http://www.stolaf.edu/people/hansonr/jmol/docs/examples
>
> I plan to write a few more documentation pages--I haven't taken a close
> look at all the /samples/ files yet to see what I've missed, but I'm
> figuring on one relating to lighting
The lighting commands are quite hard to control.
I would like to come up with three predefined lighting options
(soft/medium/hard?), then offer them as script commands. Otherwise playing
with the individual settings is just too difficult for people to control.
for example, try the following:
cpk on;
set ambient 30; set diffuse 80; set specpower 80; set specpower -7
the balls look harder and more ceramic, instead of soft.
The negative specpower has an impact on the size of the specular hilite.
I encourage you to play with it. Record the settings that you are using.
Try to create another one or two that you like.
Note that specpower can also take a
> and, basically, each of the "set"
> command groups I've identified. This breaking the set command into parts
> seems to have worked quite well. Hope you agree. Please tell me if I've
> misplaced commands within these groups. I was thinking a few choice
> thumnails for the trace,cartoon, etc., would be nice.
That is a very good idea, esp for beginners. Choose a small .pdb file. I
always use 1CRN.pdb ... but if you have a favorite then go ahead and use
it. Whatever you choose should have both beta-sheet and alpha-helix.
> I'd like someone to explain the solvent "probe radius" -- I know what it
> is, just now how to describe how to turn it on and display it properly.
OK ...
There probably are some URL references in the source code. Presumably
Connolly has a good definition that he worked on for a long time.
> Have I got scale3d right?
scale3d sets an absolute ratio of pixels/angstrom. To be chime-compatible,
the ratio is set as angstroms/inch ... where Jmol assumes 72 pixels/inch.
If there was any value, I would be willing to get rid of the references to
inch and change it to 100 pixels. Then we could stay in the metric system.
Then it would be setting angstroms/100 pixels
Probably nobody cares.
> Our computer system is going down for the weekend.
OK.
I will be travelling next week & will not be available via email.
Miguel
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