Richards Center at Yale University |
RC Home | Search | Table of Contents | General Information |
Last Modified: Thursday, 23-Oct-2008 15:51:52 EDT
Back to OS DescriptionIt is observed that using the test data in the OS distribution, different results are obtained with V6 (SGI) and V7.2.3 (PC/linux). (see Bottom Line.)
The differences occur in the first step, generating the dot surface. The program ds/ds72 is repeatedly invoked from main/main72, which is the first program invoked by the os.run script.
ds reads part_i.pdb and generates part_i.ms.
part_i.pdb is a fractional pdb file, containing all the atoms in a single residue, plus the N from the next residue, and the C from the previous residue.
part_i.ms describes the molecular surface of these atoms. See examples below. For each atom, there is an atom record, followed by records for each dot on the atom's surface. Area is the dot's area. Code, for linux, is ST followed by a single digit (dot_ISHAPE) which is probably a code for convex, concave, saddle, etc.
|- atom/dot coords ---| code area |-surface normal --| First 5 lines SGI: ARG 1 CA 5.320 5.998 -10.170 A ARG 1 CA 3.449 6.234 -9.941 SC0 0.214 -0.985 0.124 0.121 ARG 1 CA 3.543 5.998 -9.496 SC0 0.214 -0.935 0.000 0.355 ARG 1 CA 3.604 5.538 -9.496 SC0 0.214 -0.903 -0.242 0.355 ARG 1 CA 3.604 6.458 -9.496 SC0 0.214 -0.903 0.242 0.355 First 5 lines Linux: ARG 1 CA 5.320 5.998 -10.170 A ARG 1 CA 3.402 6.070 -10.556 ST3 0.186 -0.957 0.278 0.087 ARG 1 CA 3.472 6.446 -10.704 ST3 0.184 -0.982 0.129 0.140 ARG 1 CA 3.433 6.206 -10.592 ST2 0.056 -0.967 0.241 0.087 ARG 1 CA 5.196 4.113 -9.744 ST3 0.101 -0.002 -0.871 0.491Differences between ds (SGI V6) and ds72 (Linux V7.2.3):
It is hardly surprising that they give different results. One suspects that 7.2.3 gives better results because of a more sophisticated treatment of each surface dot.
The results of subsequent steps in the OS script also differ between the two versions. This is hardly surprising, because they are based on the .ms filers generated by ds/ds72.
Last Modified: Thursday, 23-Oct-2008 15:51:52 EDT
RC Home | Search | Table of Contents | General Information |
Richards Center (www.rc.yale.edu) at
Yale University (www.yale.edu)
Contact: michael^strickler_at_yale^edu |