> programs. So I am in search of a solution. Can one manually create a > secondary structure assignment matrix to insert into the PDB file? I must > admit that as a novice I do not understand the formatting of the secondary > structure matrices that I have seen embedded in some PDB files. Is there a > resource somewhere that explains the formatting of such a matrix?
I've been fiddling with this for my own work; I wrote a parser in Perl to embed structural annotation in a PDB file based on output from DSSP, STRIDE, or RasMol. Unfortunately it doesn't handle multiple chains yet, but I'm working on making it more general. I suppose since I only use this for loading files into PyMOL, I could just write it in Python as a PyMOL module. . . would that be useful to anyone else? The complete PDB specification for SS annotation is here: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_42.html http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_44.html http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_45.html However, PyMOL's built-in commands end up being much easier to use... I wish I'd realized that before I wrote my parser. > Alternatively, is there a manual series of Pymol commands to directly assign > secondary structure for a protein for insertion into the .pml script file? alter atom_selection, ss='L' (or 'H' or 'S', I think) > Even better, is there a separate program that can assign secondary structure > and then allow you to save the revised PDB file with the secondary structure > assignments inserted into the PDB output. I would be willing to accept any If there is, I'd like to know too! -Nat Echols Gerstein Lab Yale University
