>> 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? >> 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 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? Miguel ------------------------------------------------------- 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
