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#216 - 10/23/03 05:26 AM asa-protein.str
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
*FILENAME: asa-protein.str
*PURPOSE: compute Lee-Richards type accessible surface area of a protein probe radius 1.4A
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
*
!RETURNS:
! ASA computed for the selection defined as SOLUTE (which also gives the context to be used)
! is returned in variable ASA
! One could extend this to subdivide the calculation based on atom or aa type
!ASSUMPTIONS:
! psf and coordinates in MAIN coordinate set
! selection SOLUTE defined
!USAGE EXAMPLE
! read rtf,para,psf, coor
! define SOLUTE sele segid prot end
! stream asa-protein.str

coor surf rprobe 1.4 select SOLUTE end
! ASA per atom is now in WMAIN array, sum up over selected atoms
scalar wmain statistics select SOLUTE end
set ASA ?STOT
!scalar wmain statistics select "NONPOLAR" end
!set ASANP ?STOT

return
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#217 - 03/18/09 09:51 AM Re: asa-protein.str [Re: lennart]
nqn Offline
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Registered: 02/03/09
Posts: 40
Loc: France
Hi,
I would like to know which residues are accessible by the solvent. Is it possible with this script (if I understand correctly, this script returns only area of solute accessible, isn'it?)?

Thanks for advice!

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#218 - 03/18/09 09:57 AM Re: asa-protein.str [Re: nqn]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Yes. The key is here:
coor surf rprobe 1.4 select SOLUTE end
! ASA per atom is now in WMAIN array,
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#219 - 03/18/09 10:12 AM Re: asa-protein.str [Re: lennart]
nqn Offline
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Registered: 02/03/09
Posts: 40
Loc: France
yes but how may I see to WMAIN?

Sorry...

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#220 - 03/18/09 10:43 AM Re: asa-protein.str [Re: nqn]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
write/print coor ...
or
scalar ...
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#221 - 03/18/09 10:53 AM Re: asa-protein.str [Re: lennart]
nqn Offline
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Registered: 02/03/09
Posts: 40
Loc: France
thanks a lot Lennart! Area per atom correspond at the last column? Unit is AČ?

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#222 - 03/18/09 10:55 AM Re: asa-protein.str [Re: nqn]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
Correct
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Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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