PyMOL Documentation Trace: » b . Table of Contents. b (temperature factor ) Usage. Examples. Notes. See Also. Plus. b (temperature factor ) “ b ” selects atoms based on their temperature factor property. Usage. b > value b b = value) Examples. indicate b > 30 indicate b b = 0), These methods can approximate real b – factors . If you have an ensemble of structures (e.g. from an MD simulation) you could also calculate the root mean square fluctuation per atom (RMSF), which is related to the b – factor in the sense that it describes a distribution around a center position.
Subject: [ PyMOL ] B-factor putty tube representation Hi, I would like to define the radius of the cartoon putty on absolute, rather than a relative scale. Is there any way to do this? If I am comparing rmsd, for example, I would like every image to be representative of the true RMSD differences, rather than being a unique relative scale for each …
9/29/2014 · Here are some lesser-known PyMOL tricks that let you do some pretty cool (and useful) things: 1. Display B – factors . If you want to see the “ b – factor putty” view where the backbone is displayed as a tube with a diameter correlated to the b – factor of the structure, simply click the Action button of the object (the “A” button); mouse to “preset”; and select “ b – factor putty.”, Lists some B – factor statistics Methods The residue names, numbers and some B – factor statistics are listed. For each residue you see the average B – factor for backbone atoms, side chain atoms, and all atoms. Protons are excluded from the calculations if present. The B – factor .
11/1/2014 · The B-factors in the PDB file are calculated as B = 8? 2 where is the isotropic ADP that represents the mean square displacement from the atom’s mean position (see http://www.cmbi.umcn.nl/bdb/theory/ for an extensive explanation of the theory behind the determination of B -factors in X-ray crystallography).
Finally, you can use TLS refinement to extrapolate anisotropic B-factors. This treats entire molecules, or defined sections of a protein, as a rigid body and models its motions, and adds an…
RasMol, Jmol, Avogadro, Open Babel, BALL
