[Chimera-users] command 'buriedArea' - question

[Harinath]

Dear Tom,
                      Here is the reply log when I used the 'measure  
buried' command in a modeled complex. What am I missing in the pdb  
file and how erroneous are the calculations?

Please find the pdb file at the bottom to repeat the error.
______________________________________
Calculation of some surface components failed.  Using only single  
surface component.  This may give inaccurate areas if surfaces of  
either set of atoms or the combined set are disconnected.
Buried solvent accessible surface area = 1333.97 (A1 = 10302.4, A2 =  
7673.48, A12 = 15307.9)
Buried solvent excluded surface area = 818.456 (A1 = 8044.45, A2 =  
6390.68, A12 = 12798.2)
______________________________________

Sincerely,
Hari


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On Aug 11, 2009, at 11:11 PM, Tom Goddard wrote:

> Hi Hari,
>
> open 1a0m
> measure buried :.A :.B
>
> This measures the buried area between chains A and B.  Here's the  
> measure command documentation
>
>   http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html
>
> and some info on how to specify different sets of atoms
>
>   http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html
>
> Tom
>
>
>
> -------- Original Message --------
> Subject: [Chimera-users] command 'buriedArea'
> From: Harinathachari Bahudhanapati
> To: chimera-users at cgl.ucsf.edu
> Date: 8/11/09 7:59 PM
>> Hi all,
>>         Could you explain the command 'measure buriedArea' ? I am  
>> trying yesterday's daily build. Could you give me an example how to  
>> use this command? I think I am mangling the command, somehow. Could  
>> you help me?
>>
>> Thank you very much.
>>
>> Sincerely,
>> Hari
>>
>