In theory, BSA is easy, if one is looking for just a general idea. Otherwise, it may get complicated. The formula you present gives "twice" the BSA, depending of the definition you are looking for. There are also other ways to calculate the BSA. The BSA is also dependent on the probe size.
João On Mon, Apr 4, 2016 at 11:46 AM, Fotis Baltoumas <fotis.baltou...@gmail.com> wrote: > Hello, > > While there is no ready-to-use buried surface area (BSA) calculation > command, it is extremely easy to do it yourself. Just calculate the > accessible surface area (ASA) values (see the Get_Area command on how to do > that: http://www.pymolwiki.org/index.php/Get_Area) for the entire complex > and its isolated components and then simply do a subtraction. e.g., for > two proteins A and B, that form a protein-protein complex, AB, the contact > surface area would be: > > BSA = ASA(A) + ASA(B) - ASA(AB) > > For the angle, try installing the psico module ( > http://www.pymolwiki.org/index.php/Psico). It introduces a number of > geometry related functions, including one called "angle_between_domains", > which basically does what the name says. > > 2016-04-04 12:24 GMT+03:00 Smith Liu <smith_liu...@163.com>: > >> Dear All, >> >> Will you please tell me the command to calculate the contact surface area >> between 2 sub-units in the protein complex? Will you please also tell me >> the command to calculate the angle in degree between 2 domains in a >> sub-unit? >> >> Smith >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 > -- João M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613
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