Hi Kingsley, The b-factor is a result of the X-ray crystallography experiment. If you have X-ray data, I suggest to consult the CCP4BB mailing list (http://www.ccp4.ac.uk/ccp4bb.php). If you don’t have such data, then you can’t calculate a b-factor.
There are computational methods which analyze a structure for potential flexibility, for example Normal Mode Analysis (NMA). 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. See for example “rmsf2b” in the PSICO library: https://github.com/speleo3/pymol-psico/blob/master/psico/editing.py#L69 Cheers, Thomas > On May 8, 2017, at 2:42 PM, Kingsley Theras Primus Dass . > <105726...@gms.tcu.edu.tw> wrote: > > Hi everyone ! > I want to calculate the b-factor for my protein . Can. Anyone tell me how to > do b-factor or some tutorial about that. > > Thanks in advance :) -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
