This message is about graphical renderings of the 'temperature/B-factor' value.
I previously exchanged a few emails offlist with Jan regarding the interpretation of 'temperature' values for the graphic rendering of 'trace temperature'. 'trace temperature' shows a snake/worm rendering where the diameter is a function of the temperature/B-factor of the alpha carbon atoms. The implementation in RasMol was to scale these values based upon the min/max temp values of the alpha carbon atoms found in the file. Jan suggested the following: > I would suggest to use the resolution, if you want to do scaling. But > I'm not a specialist so I cite Bernhard Rupp: > >>Isotropic B is defined as 8*pi**2<u**2>. >>Meaning: eight pi squared =79 >>so B=79*mean square displacement (from rest position) of the atom. as >> u is in Angstrom, B must be in Angstrom squared. >> >>example: B=79A**2 >>thus, u=sqrt([79/79]) = 1 A mean positional displacement for atom. A url reference for this is: http://www.rcsb.org/pdb/lists/pdb-l/200303/000609.html (I am only a chemistry/crystallography hacker ... this was the first time I have ever seen/understood any description of temperature/B-factor.) Jan's suggestion made sense to me: If the temperature corresponds to a physical meaning (mean positional displacement) then that is the way we should render it. However, after implementing it I was not very happy with the results. There seems to be a variety of temperature values stored in .pdb files. But the resulting range of displacement values is relatively small. The range for the alpha carbon temp values in 1crn goes from 3.38 to 10.80, corresponding to mean positional displacement values of 0.21 to 0.37 Angstroms (If my calculations are correct). For 5cro the range is much higher and broader. The minimum alpha carbon temp value is 18.86. There are several in the 80's and 90's, and several with the suspiciously round number of 100.00. So the mean positional displacements range from 0.49 angstroms to 1.13 angstroms (again, if my calculations are correct). So, the problem for visualization is this. For 1crn the values are too small and the 'snake' looks too thin. For 5cro there is more variation, but even it does not have enough *range*. They are both implemented in the current CVS head of the development version of Jmol v10. For those of you who can pull down the latest build you can take a look at the two implementations. 'trace temperature' roughly corresponds to the RasMol implementation. The temperature values of the alpha carbons are linearly mapped to the range 0-100. Then these values are mapped to a 'snake diameter' of .25 to 2.0 angstroms. I added 'trace displacement' as a temporary way to implement this and for us to look at it. It calculates the mean positional displacement using the formula cited by Bernhard Rupp above. I think my questions are: Q: Is it useful to see temperature values, displacement values, or both? Q: In either case, should the values correspond to absolute diameters? Or should they be scaled relative to the values that are present in that file? Or, do you want both? Q: Any other comments or advice? Thanks, Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
