hi Miguel, it getters better - some of these are abbreviations that can be used for elements and chains. but the conflict arises from traditional nomenclature, not specifically from mol vis.
here's what I can determine from RasMol 2.6b3. on their own, the single-letter abbreviations are *only* usable for nucleotides. I don't think they can be used to select residues at all. for example, in 1d66.pdb which has both protein and dna: # is this cystine, cytosine, or carbon? no way to tell. select c 260 atoms selected! # # try to select cystine only. select protein and c No atoms selected! select protein and cys 72 atoms selected! # # try to select cytosine only. select nucleic and c 260 atoms selected! # note this is the same as *select c* above. select nucleic and cytosine No atoms selected! select nucleic and cytidine No atoms selected! # note that cytosine is only accessible via its single-letter abbrev. # the situation for the letter C in particular is much more complicated, since C can refer to carbon as well. in that case, it is used with a modifier like '*.ca' to select alpha carbons. hope that helps, :tim -- timothy driscoll molvisions - molecular graphics & visualization <http://www.molvisions.com/> usa:north carolina:wake forest at 9:26 pm EDT on (Tuesday) 21 October 2003 Miguel said: > Based upon reading the documentation, the RasMol scripting language has > several ambiguities. One of them is a conflict in predefined sets. > > Amino acids have three letter abbreviations & 1 letter abbreviations > a = ala -> alanine > c = cys -> cystine > g = gly -> glycine > t = thr -> threonine > ... > > I also see that the predefined sets for the 4 nucleotide bases are > a -> adenosine > c -> cytidine > g -> guanosine > t -> thymidine > > Can anyone shed any light on how this ambiguity is handled at run-time? > > In practice, do people *use* the single letter amino acid abbreviations in > scripting? > > Miguel > > > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by OSDN developer relations > Here's your chance to show off your extensive product knowledge > We want to know what you know. Tell us and you have a chance to win $100 > http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 > _______________________________________________ > Jmol-developers mailing list > [EMAIL PROTECTED] > https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------- This SF.net email is sponsored by OSDN developer relations Here's your chance to show off your extensive product knowledge We want to know what you know. Tell us and you have a chance to win $100 http://www.zoomerang.com/survey.zgi?HRPT1X3RYQNC5V4MLNSV3E54 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
