>> This might make it somewhat easier ... in fact, most of the data >> structures to support this are already in place. >> > then perhaps we don't need to read the MODRES at all.
I think that would be good. Esp if MODRES records are often missing from .pdb file. > as long as Jmol > can separate modified residues from covalently-bound ligands. I do not understand >> I also build a data structure called viewer.pdb.PdbPolymer which is >> similar, but not the same. It is the data structure for a real >> *chain*. >> > we spoke about polymer vs chain in the autumn, as I recall. this sounds > like a Very Useful Thing. Correct, you helped me figure this out ... leading to dramatic/breathtaking code restructuring :-) >> In order for a residue to make it into a PdbPolymer it needs to have: >> - amino nitrogen >> - alpha carbon >> - carbonyl carbon >> - carbonyl oxygen >> >> This should happen independent of the group name. >> > sounds good. the alpha carbon should be easy; it has a unique > identifier CA. Unfortunately, many .pdb files do not follow the PDB spec. The current code tries to be flexible and will accept the first 'C' as a 'CA' > the other three are simply defined as N, C, and O. in > standard amino acid residues this is a non-issue - since all other atoms > are well-defined by their chemical position (CB, NZ, OD1, OD2, etc.), > the backbone atoms are obvious. I'm not sure this is true for modified > residues - I'll have to check the PDB spec. > > > >> Here is how you can test this out: >> 1. load up a model that has a modified residue >> (with or without a MODRES record ... >> this record type is currently ignored) >> 2. turn on backbone >> 3. see whether or not the residue appears in the backbone >> >> If it does, then most of the work is done. >> > ok; I'll check. > > >> Q: Can you please add a small file that contains a modified protein >> residue to the samples directory ... with a name like >> modifiedProteinResidue.pdb >> > will do this. Eric has recommended that we start holding on to strange/test cases. Let's organize this a little better by creating some subdirectories: samples/pdbtest/modifiedGroup Put your sample files in there, with their pdbId names. We'll add other test cases to sibling subdirectories. >> you said: >> > anything with an alpha carbon and amino group bound in the >> > backbone of a protein chain would be considered protein >> >> Q: Are there cases where something can get into the protein chain >> without having >> N-C-C=O ? >> > yes; any covalently-bound ligand. I'll scare up some examples from the > PDB. OK, stick them in the modifiedGroup subdirectory (or another subdirectory of pdbtest if that is better) Something for you to think about ... What happens to backbone/trace/strands/ribbons/cartoons when you stick one of these 'covalently-bound ligands' in the pdbpolymer? >> Q: If so, what are the criteria for determining whether or not >> something is in the polymer chain? >> > assuming you mean the PDB criteria, I'll have to look. Actually, I didn't mean the PDB criteria. I think you gave the answer above ... 'any covalently-bound ligand' > I'll get back with you after doing some more research. Good Miguel ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
