Hi all, among others there are the following predefined residue sets available in Jmol: "amino" and "protein".
The documentation at "http://chemapps.stolaf.edu/jmol/docs/"; states that "amino" is defined as "all twenty standard amino acids, plus ASX, GLX, UNK". For "protein" it states as definition "defined as a group that contains PDB atom designations C, N, and CA". A few weeks ago Bob explained that there is an additional condition for "protein": contains PDB atom designations O or O1. And if all residues contain only CA atoms they are also put into the "protein" set (e.g.: 1A1D). This means that the "amino" set is restricted to standard amino acid residues while the "protein" set also includes modified amino acid residues. But there are for example PDB entries where only C,N and CA atoms are present for standard amino acid residues (e.g.: 1L9U). These are put into the "amino" set but not into the "protein" set. Q: Why are residues that are recognized by their name as standard amino acid residues not also put into the "protein" set irrespective of the atoms that are available? If a standard amino acid residue only contains C,N and CA atoms there is no "trace" or "cartoon" drawn. In the case of "1L9U" nothing is drawn at all. In other cases where only some residues don't have oxygens the "trace" and "cartoon" is disrupted. Q: Is the missing cartoon/trace a consequence of the missing classification as protein or are there other reasons? ---- Test System ---------------- Jmol: 11.3.47, application Java: 1.4.2_13 OS : Linux, SuSE Enterprise 10 --------------------------------- Regards, Rolf ------------------------------------------------------------------------- SF.Net email is sponsored by: The Future of Linux Business White Paper from Novell. From the desktop to the data center, Linux is going mainstream. Let it simplify your IT future. http://altfarm.mediaplex.com/ad/ck/8857-50307-18918-4 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
