at 9.17a EDT on 2004 February 25 Wednesday Miguel Howard said: > Egon wrote: > > > Would coloring by B factor be appreciated much? It's easy to add... > > Coloring by B factor currently should work for .pdb files. But this > probably needs to be generalized to other file types ... added to the > JmolModelAdapter API. > > Q: Can someone give me a 1 paragraph description of B factor? > > Within the RasMol/PDB world there seems to be some confusion between B > factor and temperature. I believe that someone told me that they were not > the same thing. > > Q: Can someone give me a 1 paragraph description of 'temperature' ? >
well, I'm no expert in crystallography so I went to the expert that I know. the following is quoted from the Web site of Gale Rhodes author of "Crystallography Made Crystal Clear": <http://www.usm.maine.edu/~rhodes/ModQual/index.html#Temperature%20factor%20( crystallogr> " The temperature factor or B-factor can be thought of as a measure of how much an atom oscillates or vibrates around the position specified in the model. Atoms at side-chain termini are expected to exhibit more freedom of movement than main-chain atoms, and this movement amounts to spreading each atom over a small region of space. Diffraction is affected by this variation in atomic position, so it is realistic to assign a temperature factor to each atom and to include the factor among parameters to optimize during least-squares refinement. From the temperature factors computed during refinement, we learn which atoms in the molecule have the most freedom of movement, and we gain some insight into the dynamics of our largely static model. In addition, adding the effects of motion to our model makes it more realistic and hence more likely to fit the data precisely. " (the entire glossary can be found at <http://www.usm.maine.edu/~rhodes/ModQual/index.html>). hth, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id56&alloc_id438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
