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Dear Sreetama looking at your pdbs, I would say that the only choice you have is to get a feeling on things. Indeed, it will be difficult to put numbers on flexibility of elements coming from different crystals, i.e. different crystal conditions, crystal packing, solvent, amino acid composition etc. What could be done though is to get a hint on the relative flexibility of the elements, by comparing the B-factors the pdbs individually. Convert all the B-factor values in each pdb in %age, and you can (to some extends) compare the flexibility of regions when compared to other ones. Not sure if there is any tool to do so; it would be quick enough to write up a small python script to do so. Probably visualisation software (e.g. PyMol) have a colouring scheme for that as well. Cheers, leo > On 10 Feb 2016, at 08:54, sreetama das <[log in to unmask]> wrote: > > Dear All, > > I would like to compare the flexibility of the secondary structure elements forming the active site in homologous proteins. What are the possible methods of doing it? Not all the homologs have high sequence similarity (<50% similarity). > > I have looked at some older threads on the BB regarding usage of B-factors. While some have suggested the addition of a constant to the model with the lower B-factors to compare to the one with other B-factors, others have commented that it is not valid to compare B-factors for data collected from different crystals. > > Also, B-factor based-analysis can't be carried out when the homologs have NMR structures. > > Any suggestions? The tools may also include software/servers outside the CCP4 suite . > > Looking forward to your replies, > > Thanks and regards, > Ms. Sreetama Das > PhD student, > Dept. of Physics, > Indian Institute of Science - Leonard Chavas - Synchrotron SOLEIL Proxima-I L'Orme des Merisiers Saint-Aubin - BP 48 91192 Gif-sur-Yvette Cedex France - Phone: +33 169 359 746 Mobile: +33 644 321 614 E-mail: [log in to unmask] -