Rolf, thanks for spotting this. It was a bug. Fixed for 11.3.51 Rolf Huehne wrote:
> 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". > > > that's required for RasMol compatibility >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). > > here we have taken the liberty of expanding upon the RasMol definition, which I see from the OpenRasMol code is based solely upon name: #define IsAmino(x) ((x)<=23) ... #define IsProtein(x) (((x)<=23) || (((x)>=43) && ((x)<=45))) Those extra three there for protein are UNK, ACE, and FOR Which doesn't exactly make sense to me, since ACE could be acetyl group; acetic acid; acetate ion based on http://atb.csb.yale.edu/xplor/hetero/ACE.html and FOR is a carbamyl activator group based on what I see at http://atb.csb.yale.edu/xplor/hetero/FOR.html >This means that the "amino" set is restricted to standard amino acid >residues while the "protein" set also includes modified amino acid residues. > > > and "amino" is the same as RasMol, but "protein" is not. >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. > > > this was a bug fixed in 11.3.51 -- you also could not use cartoons and traces and such with them; >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? > > > it was a bug >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. > > > this was a bug -- fixed >Q: Is the missing cartoon/trace a consequence of the missing >classification as protein or are there other reasons? > > missing classification -- fixed >---- 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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
