Jose,
Your are most probably right.
Atoms used for ASA calculations are "unified atoms" as their vdW radii
incorporate light atoms (hydrogens) which, by and large,
crystallographers don't see.
Adding extra H atoms is likely to end up in miscalculations.
Nadir Mrabet
Pr. Nadir T. Mrabet
Structural & Molecular Biochemistry
N-gere - INSERM U-954
University of Lorraine, Nancy
School of Sciences and Technologies
& School of Medicine
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On 28/07/2014 14:20, Jose Manuel Duarte wrote:
I believe that ignoring hydrogen atoms is the default behaviour of any
software calculating ASA values. Normally the VdW radii values of the
heavy atoms already include the hydrogens implicitly.
If your input structure has hydrogens and they were included in the
calculation it would result in over-estimating the ASA values. I'm not
familiar with AREAIMOL but I guess it must behave in a similar way.
Jose
On 28/07/14 14:02, Harry Mark Greenblatt wrote:
BS"D
Dear All,
I understood from the areaimol documentation that hydrogens are
not included as one of the default atoms. But one can add atoms, and
so I added an "ATOM" line for hydrogen. The program quite happily
accepted my input line, but later on stated explicitly that it was
ignoring the hydrogens. Is there no way to include hydrogens?
Thanks
Harry
-------------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Weizmann Institute of SciencePhone:972-8-934-3625
234 Herzl St. Facsimile: 972-8-934-4159
Rehovot, 76100
Israel
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