Re: [ccp4bb] interface

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Refmac out-put file header information
From: Yusuf Akhter yusuf {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-08-08

Next message:
Subject: Re: interface
From: Steven Darnell sdarnell {- at -} BIOCHEM {- dot -} WISC {- dot -} EDU
Date: 2008-08-08

Subject: Re: interface
From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU
Date: 2008-08-08

Which brings up something about PISA. If I run PISA on pdb entry 2IE3,
which I'm familiar with, I get the following numbers from PISA and
CCP4's AREAIMOL (surface areas in Angstrom^2) for the A:C interface.

>> PISA for 2IE3
Automatic A:C interface selection 907.9
(a crystal packing interface is larger than this, but this surface
is the A:C interface)

>> AreaIMol with some editing of 2IE3 to separate the chains
Chain A 25,604.4
Chain C 11,847.4
Total 37,451.8
Chain AC 35,576.6
Difference 1,875.2
Difference/2 937.6

For buried S.A. I agree with Steve Darnell's definition. However PISA
appears to be reporting half that value, or what it calls "interface
area". Potentially confusing.

Phil Jeffrey
Princeton

Steven Darnell wrote:
> Sorry, that equation should read:
>
> Buried_Surface_Area = ASA_unbound1 + ASA_unbound2 - ASA_bound
> ASA = Accessible Surface Area
>
> The way I wrote it before would give you a negative value.
>
> Regards,
> Steve Darnell
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Refmac out-put file header information
From: Yusuf Akhter yusuf {- at -} EMBL-HAMBURG {- dot -} DE
Date: 2008-08-08

Next message:
Subject: Re: interface
From: Steven Darnell sdarnell {- at -} BIOCHEM {- dot -} WISC {- dot -} EDU
Date: 2008-08-08