[Jmol-developers] documentation

[Bob H. <ha...@st...>]

I'm almost done (I think) with script documentation. Take a look at

http://www.stolaf.edu/people/hansonr/jmol/docs


and in

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 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.

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.

Have I got scale3d right?

Our computer system is going down for the weekend.

Bob



SourceForge.net wrote:

>Bugs item #974437, was opened at 2004-06-17 02:56
>Message generated for change (Comment added) made by interessent
>You can respond by visiting: 
>https://sourceforge.net/tracker/?func=detail&atid=379133&aid=974437&group_id=23629
>
>Category: Algorithms
>Group: None
>Status: Closed
>Resolution: Fixed
>Priority: 5
>Submitted By: Nobody/Anonymous (nobody)
>Assigned to: Miguel (migueljmol)
>Summary: cpk temperature
>
>Initial Comment:
>cpk temperature does not relate well to Rasmol. A
>comparison using 1a3n shows Jmol giving a cpk
>temperature radius far too large--at least in
>comparison to Rasmol 2.6.
>
>Bob Hanson
>
>
>----------------------------------------------------------------------
>
>Comment By: JR (interessent)
>Date: 2004-06-18 06:10
>
>Message:
>Logged In: YES 
>user_id=908382
>
>but in principle the bfactor scheme should be applicable to
>atom radius, too, and Bob is right, the values in 1a3n are
>30.00 and not 3000 (which I generated by using RasMol2.7.2
>label %b command - Jmol does this labeling right :-)
>
>
>----------------------------------------------------------------------
>
>Comment By: Miguel (migueljmol)
>Date: 2004-06-17 22:17
>
>Message:
>Logged In: YES 
>user_id=1050060
>
>Actually, Jan's comment was related to trace temperature,
>not cpk temperature. 
>
>The RasMol doc clearly states that the temperature value is
>directly applied to the atom radius ... with a maximum
>radius of 2.0. 
>
>So I went ahead and implemented it to be RasMol/Chime
>compliant. 
>
>
>
>----------------------------------------------------------------------
>
>Comment By: Miguel (migueljmol)
>Date: 2004-06-17 08:40
>
>Message:
>Logged In: YES 
>user_id=1050060
>
>Q: Should we use the term 'temperature' for RasMol
>compatibility and the term 'bfactor' for mean positional
>displacement? 
>
>
>----------------------------------------------------------------------
>
>Comment By: JR (interessent)
>Date: 2004-06-17 07:38
>
>Message:
>Logged In: YES 
>user_id=908382
>
>this is a feature, not a bug. RasMol scales relative to a
>maximum while Jmol should approximate the mean positional
>displacement
>sqrt(B / 79)
>In 1a3n B is e.g. several thousand sqrt(3000/79)= 6 A
>but RasMol only scales them to a maximum of ~3 A
>
>----------------------------------------------------------------------
>
>You can respond by visiting: 
>https://sourceforge.net/tracker/?func=detail&atid=379133&aid=974437&group_id=23629
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by The 2004 JavaOne(SM) Conference
>Learn from the experts at JavaOne(SM), Sun's Worldwide Java Developer
>Conference, June 28 - July 1 at the Moscone Center in San Francisco, CA
>REGISTER AND SAVE! http://java.sun.com/javaone/sf Priority Code NWMGYKND
>_______________________________________________
>Jmol-developers mailing list
>Jmo...@li...
>https://lists.sourceforge.net/lists/listinfo/jmol-developers
>  
>

-- 

-- Robert M. Hanson, ha...@st..., 507-646-3107 
Professor of Chemistry, St. Olaf College 
1520 St. Olaf Ave., Northfield, MN 55057 
mailto:ha...@st... 
http://www.stolaf.edu/people/hansonr