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 [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
