> Yes, please. There are some structures that have to be generated by using > symmetry operations defined in the "REMARK 350" lines in the pdb file > (example: > 1jjy.pdb). The only way (I know of, if you know a better one, please tell me) > to > do this is going to http://pqs.ebi.ac.uk where the complete structure is > generated for you. However, the caveat is: This service removes the secondary > structure information, and up to now I have manually copy-pasted it into the > new > pdb file (Annoying work, really).
Unfortunately, the script I came up with won't deal with that; it basically uses a third-party program to rescan the input file and uses the alter command to correctly set the structure (or combines this with file loading as a single command). If anyone would like this, I'm happy to email it to them, but it's not really a good general solution. How hard would it be to incorporate the DSSP algorithm? I was looking at the source for RasMol, which has a complete implementation. My feeling is that this could be ported without too much misery. However, RasMol's license terms are different, and I suspect even a complete translation into Python with the ChemPy API would still be considered a "derivative work", meaning it wouldn't be able to be part of the main distribution, and meaning someone would still have to code DSSP from scratch. (I have utterly no idea how it works, but RasMol's code seems clear enough despite lack of comments) -Nat
