Re: [PyMOL] on contact surface and domain angle
Hi, On 4/4/16 6:04 PM, João M. Damas wrote: > formula you present gives "twice" the BSA, depending of the definition Agreed on all points, except that by my reading of the literature (since the days of Chothia and colleagues, 1970s through this century), the definition for BSA (or more accurately, total BSA) is the surface area buried on both (or all) components. So, Fotis' formula is accurate, in my opinion. CCP4's PISA defines an "interface area" that matches your definition (unfortunately, that term has also been used inconsistently in the literature). Happy to be corrected if I'm wrong on this. For the reasons you have stated on different ways to calculate BSA such as the solvent probe radius, I would use a published package, such as PISA, for calculating BSA (and multiply the "interface area" by two :) ) if I intend to publish that number. Engin -- ___ 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
Re: [PyMOL] on contact surface and domain angle
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 Baltoumaswrote: > 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 : > >> 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 -- ___ 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
Re: [PyMOL] on contact surface and domain angle
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: > 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
[PyMOL] on contact surface and domain angle
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