> Ideally util.ss could become a shell that would know (from the environment?) > if dssp or similar was installed, then either run dssp and parse the output > to assign the ss, or else run the ss asignment code in the current util.ss if > no other options were available.
I've basically done this, though right now it uses STRIDE because the output is easier to parse- it just uses popen2() to read the output from the STRIDE executable (Does anyone actually know what the difference is between these two programs?). But since I already wrote a dssp parser in Perl, it shouldn't take long to modify. My feeling is that it would be better to have a robust secondary structure algorithm built in, since I've already hit limitations in the method I'm using. Though to be honest, I've been getting away with using util.ss for some time now. > The ability to write a pdb with the newly generated ss information would be > useful as well (or perhaps pymol already can do this if it knows the > protein's ss?). I've done this too, though I think it breaks with more than one chain right now. If I get around to cleaning this up I'd be more than happy to pass it on. -Nat
