at 10.22a EDT on 2004 February 11 Wednesday Miguel Howard said: > > 2. I need some advice on how to proceed with fixing the predefined set > > 'protein'. should I try to include all of the known modified residue > > names in the JmolConstants file? seems like an awful kludge, though > > maybe that's the only way. > > [...] > > in an ideal world, Jmol would read the MODRES records and add the > > contents to the protein set. > > OK, I just read the spec on MODRES. It doesn't seem too bad. The only > issue is that there currently are no data structures that describe these > 3-letter residue names. The only real attribute they have is their > position in JmolConstants.predefinedGroup3Names ... > > > by default (esp for files with no MODRES > > records), anything with an alpha carbon and amino group bound in the > > backbone of a protein chain would be considered protein. > > 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. as long as Jmol can separate modified residues from covalently-bound ligands.
> I build a data structure called viewer.pdb.PdbChain which exactly > corresponds to the chain specifications in the .pdb file. A 'chain' in > this context can contain HETATMs, water, etc. > yes, this poses problems when, for example, waters are included in a PDB chain along with protein. or a ligand not covalently bound to a chain is giventhe same chain designation (to indicate association). > 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. > 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. 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. > 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. > 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. > Q: How important are modified residues? > very. of course. ;-) > > is this a reasonable task? > > I think this is a good task for us to implement together. > It would be very helpful for you to run the tests above. > I will probably need to make at least some of the modifications to the > data structures because they will be somewhat complicated. > ok, that sounds good to me. I'll get back with you after doing some more research. regards, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- 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
