Re: [PyMOL] on contact surface and domain angle

[Engin Özkan]

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

[João M . Damas]

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 
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 :
>
>> 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

[Fotis Baltoumas]

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

[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