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:
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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 :-)
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Comment By: Miguel (migueljmol) Date: 2004-06-17 22:17
Message:
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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.
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Comment By: Miguel (migueljmol) Date: 2004-06-17 08:40
Message:
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Q: Should we use the term 'temperature' for RasMol
compatibility and the term 'bfactor' for mean positional
displacement?
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Comment By: JR (interessent) Date: 2004-06-17 07:38
Message:
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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
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