Dear Modeller users & developers,

I would like to use the capability of modeller to calculate different kind of solvent accessibility data with the WRITE_DATA command. I can get the *.psa file and the *.sol file using the script shown below (practically identical with the example in the manual). Now my questions:

o what are the units of the numbers given in the *.psa file? I suppose that the "Sum" coloumns give the accessible surface in square Angstrom. The "Per." coloumns are supposed to the accessible surface area in percent of the total surface? Why do I get values above 100 in many cases then?

o How should the ACCESSIBILITY_TYPE parameter of WRITE_DATA be used to write different kind of accessibility dat to the Biso coloumn of the *.sol file? As far as I understand the manual the ACCESSIBILITY_TYPE parameter can be used to influence this part of the *.sol output file? I tried various things without any effect.

o What are the numbers written to the *.sol file with the script below?

Thanks a lot in advance, Oliver ____________________________________________________________

Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific Ave Seattle, WA 98195 T:(206)685-7046 _______________________________

My input script: ------------------------------------------------------------ SET OUTPUT_CONTROL = 1 1 1 1 0

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' SET HETATM_IO = off, WATER_IO = off

READ_MODEL FILE = 'protein'

SET RADII_FACTOR = 1.0

WRITE_DATA FILE = 'protein', OUTPUT = 'PSA' --------------------------------------------------------------

Start of the protein.psa file: -------------------------------------------------------------- #COLUMNS S S S N N N N N N N N N N # produced by MODELLER # # File of summed (Sum) and % (per.) accessibilities # probe radius : 1.400 # integration step : 0.100 # water included : ? # hetatom included : ? # accessibility type : CONTACT # number of residues : 730 # # Res Res All atoms Non P side Polar Side Total Side Main Chain # Num type Sum Per. Sum Per. Sum Per. Sum Per. Sum Per. ACCESS 55 PHE A 75.12 123.5 50.74 98.4 0.00 0.0 50.74 98.4 24.38 262.7 ACCESS 56 LEU A 19.62 34.7 16.14 34.6 0.00 0.0 16.14 34.6 3.47 35.0 ACCESS 57 SER A 20.64 61.1 11.84 75.1 7.67 97.5 19.51 82.6 1.13 11.1 ACCESS 58 LEU A 3.76 6.6 2.99 6.4 0.00 0.0 2.99 6.4 0.76 7.7 ACCESS 59 ASP A 31.28 79.4 9.54 59.8 13.93 103.7 23.47 79.8 7.81 78.3 --------------------------------------------------------------------------------------------------

Start of the corresponding *.sol file: ---------------------------------------------------------

# produced by MODELLER # # File of atomic accessibilities # probe radius : 1.400 # integration step : 0.100 # water included : ? # hetatom included : ? # accessibility type : CONTACT # number of residues : 730 ATOM 1 N PHE A 55 107.149 -1.404 53.483 1.650 14.140 ATOM 2 CA PHE A 55 106.564 -2.771 53.570 1.800 1.890 ATOM 3 C PHE A 55 106.502 -3.415 52.180 1.800 1.008 ATOM 4 O PHE A 55 107.505 -3.970 51.725 1.550 9.229 ATOM 5 CB PHE A 55 105.182 -2.745 54.253 1.800 2.554 ATOM 6 CG PHE A 55 105.162 -3.402 55.622 1.800 0.319 ATOM 7 CD1 PHE A 55 104.233 -4.411 55.914 1.800 7.619 ATOM 8 CD2 PHE A 55 106.077 -3.026 56.615 1.800 4.669 ATOM 9 CE1 PHE A 55 104.214 -5.040 57.174 1.800 11.557