at 5:36 pm EDT on (Thursday) 20 November 2003 Miguel said: > >> Does the predefined set 'at' also include 'u' ? > > > > no > > but I don't think the set at is of much use, of more interest would be > > a set pyrimidine but as far as I could see it also only contains C and > > T (and not U which I think is wrong) > So are you saying that the set pyrimidine should be defined as > define pyrimidine c,t,u > > >> Does the predefined set 'nucleic' also include 'u' ? > > yes > The RasMol 2.7.2 doc says: > > Nucleic Set > The set of all atoms in nucleic acids, which consists of the four > nucleotide bases adenosine, cytidine, guanosine and thymidine (A, C, G > and T, respectively). All neucleotides are classified as either > 'purine' or 'pyrimidine'. This set is equivalent to the RasMol atom > expressions "a,c,g,t" and "purine or pyrimidine". The symbols for RNA > nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG, OMG, YG, H2U, > 5MU, and PSU) are also recognized as members of this set. > > So, now this doesn't seem right to me. > It certainly needs to include +A, +C, +G, +T, and +I. > > Are there others that are missing? > not that I can tell.
> >> Should +A be included in the sets 'a', 'at', and 'purine' ? > > yes (but it isn't in RasMol) > > I assume that implies that +C should be included with C, and the same > for +T, +G, +U and +I > I agree. > >> I don't think there is any way to select these 'modified' residues. > > in RasMol using wild card for single character: > > select [+?] > > >> I have not tried it, but I am quite sure the Jmol expression parser > >> will not accept a '+' in this context. Do I need to fix the > >> expression parser to allow non-alpha-numeric characters as a residue > >> name? > > > > yes > > but to my knowledge + is the only exception in residue names (but > > don't burn me for that, I know less then 5% of the PDB) > > OK, I understand that + is a valid residue character and I will have to > modify the expression parser to accept it. > > Do you think there is an easy way for me to find if other characters > exist as residue name characters? > I have looked through: <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html> <http://pdb.rutgers.edu/format-faq-v1.html> <http://pdb.rutgers.edu/het_dictionary.txt> it appears that + is the only non-alphanumeric symbol used in group names; however, I can't find anything in the PDB spec that specifically limits group names to [a-z0-9+]. it might be best to inquire on the pdb list about this... :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest ------------------------------------------------------- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
