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The program: http://sb20.lbl.gov/berry/for/pdbdist2b.for does this. If you run it by the wrapper pdbd2b: echo 'Find distances greater than threshold between corresponding atoms in 2 PDB files' echo 'Usage: pdbd2b file1 file2 startres# [thresh]' pdbdist2b <<eof $1 $2 $3 10000 $3 $4 3.0 eof then the format is: pdbd2b file1 file2 startresiduenumber threshold (set the threshold to -1 to print all distances) then it is easy to redirect the output table to a textfile which can be imported to scalc or excel for plotting. It is kind of stupid: ignores chain letters, and once it finds startresiduenumber in both files it proceeds without looking at numbers or chains, so the atoms have to be in the same order in both files. But if you have an insertion deletion you can just run twice, starting after the midmatch the second time. N GLU A 13 N GLU A 13 0.0105 CA GLU A 13 CA GLU A 13 0.0092 CB GLU A 13 CB GLU A 13 0.0186 CG GLU A 13 CG GLU A 13 0.0369 CD GLU A 13 CD GLU A 13 0.0490 OE1 GLU A 13 OE1 GLU A 13 0.0623 OE2 GLU A 13 OE2 GLU A 13 0.0494 C GLU A 13 C GLU A 13 0.0231 O GLU A 13 O GLU A 13 0.0648 N THR A 14 N THR A 14 0.0156 CA THR A 14 CA THR A 14 0.0112 CB THR A 14 CB THR A 14 0.0160 OG1 THR A 14 OG1 THR A 14 0.0164 CG2 THR A 14 CG2 THR A 14 0.0273 C THR A 14 C THR A 14 0.0157 - written for g77 but seems to compile with gfortran I need to look in Dave's calendar prog to remind me how to get command lines parameters in fortran - then can dispense with the wrapper. Jacob Keller wrote: > Let me refine my question (sorry for my lack of clarity): is there a > program that will output the distances between the corresponding ca's > of a superposition on a residue-by-residue basis, and not just a > global RMSD value (doubtless these numbers are part of the > superposition algorithm itself)? I want to plot these values as a > function of residue number to show which parts of the structures > deviate more or less from each other. > > Jacob >