> 3. Jmol does not recognize DNA as a predefined set, which is easily > fixed.
Then you should do this. I have been holding off on nucleic stuff because 1) I didn't have anyone to help me with it, and 2) my outstanding grant proposal with Brian White You are now here to help/tutor me ... and we *should* be hearing something about the grant proposal pretty soon. So, as far as I am concerned, we can get started. > however, it does not recognize the RNA set either and, more > importantly, does not distinguish between DNA and RNA. this last > point is the crucial one. it is important to be able to tell the two > nucleic acids apart - something that Chime could never do properly. > (neither could Rasmol 2.6; not sure about 2.7). OK, it would be good to fix things that Chime could not do properly. Q: Are there also 'modified residues' in the DNA/RNA world? > essentially, RNA is simply 'nucleic' which contains an oxygen atom at > the 2' position on the sugar ring. DNA is 'nucleic' that does not > contain this 2' oxygen. In concept, sounds simple enough ... Q: Is it the case that the residue names do not really tell you whether they are DNA or RNA? > I'll take this on as well if you can point me in the right general > direction... Unfortunately, I fear that this is more complicated than it might seem. There currently are no data structures to work with nucleic residues. To demonstrate this, you could try select nucleic ; backbone .4 Nothing happens. Because nucleic chains are not recognized as chains. Jmol currently does not currently try to do anything special with nucleic residues ... they are no different from HOH. The first step is for us to extend PdbGroup ... PdbGroup currently has 'special' support for proteins. In particular, PdbGroup has 8 or 10 methods at the bottom which try to identify whether this group is a protein ... does it have 1. amino nitrogen 2. alpha carbon 3. carbonyl carbon 4. carbonyl oxygen If the group has all of these, then it gets to participate in a PdbPolymer. We need to build analogous support for nucleic acid residues. This is the place where we need to add the code to look for your 2' oxygen (and recognize modified nucleic acid residues) Does this make sense? 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
