Many of the predefined sets were broken in recent releases ... they are now fixed. The exceptions are:
cystine: this set represents cys residues that are part of disulfide bridges. I have done nothing on ssbonds, so this set does not work. I have several questions about 'nucleic' things. The RasMol doc is very confusing and there is no need to repeat what it says. Here are some questions: Is there a predefined set 'u' ? Does the predefined set 'at' also include 'u' ? Is there a predefined set 'au' ? Does the predefined set 'nucleic' also include 'u' ? Next set of questions ... When I look at the PDB format specification I see: RESIDUE ABBREVIATION ----------------------------------------------------------------------- Adenosine A Modified adenosine +A Cytidine C Modified cytidine +C Guanosine G Modified guanosine +G Inosine I Modified inosine +I Thymidine T Modified thymidine +T Uridine U Modified uridine +U First, with respect to Inosine: Should there be a predefined set 'i' ? Should it be included in the 'nucleic' set? Second, with respect to the 'Modified' versions: Should +A be included in the sets 'a', 'at', and 'purine' ? I don't think there is any way to select these 'modified' residues. Should there be a predefined set so that one can select them? Can you select these things in the RasMol/Chime atom expression syntax? 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? 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
