Eric wrote: > The "backbone" command in RasMol 2.6/Chime connects amino acid alpha > carbons and nucleotide phosphorus atoms for standard residues ONLY. > Non-standard amino acids can be part of an amino acid chain but are > invisible in a backbone rendering.
The Jmol behavior is somewhat different. Jmol will recognize non-standard residues, as long as they meet specific criteria. For example, a non-standard residue in an AminoPolymer must contain N-CA-C-O as the first 4 atoms. The name of the residue is not important. > This can have two undesirable consequences. > > 1. Backbone rods will be drawn between residues not connected by a peptide > bond if they are sufficiently close, skipping intervening non-standard > residues. Thus, the backbone line is incorrect. Jmol should not do this. > 2. When a standard residue is flanked by non-standard residues, it behaves > like a single-residue chain, so becomes invisible in a backbone rendering. I think that this might happen. But it depends upon how 'non-standard' the funny residues are. > Example: 1AL4 has 12 non-standard residues (D amino acids, e.g. D-leucine > DLE, D-valine DVA; note MODRES records) among 34 amino acids. The backbone > lines connect only the standard L residues, hence don't follow the actual > chemical backbone. Two standard residues are isolated between non-standard > residues. > http://molvis.sdsc.edu/protexpl/pe.htm?id=1al4 > > The covalent peptide bonds between standard and non-standard residues are > designated in 1AL4's PDB file header with LINK records (ignored by RasMol > 2.6/Chime). > > In PE, I worked around the single-residue "chain" issue by showing all > alpha carbons as spheres the same diameter as backbone rods; hence the two > isolated standard residues are not invisible. > > But Chime offers no way that I know about to correct the backbone paths > (short of modifying the PDB file). Hence in PE, the backbone lines are > incorrect in FirstView (best seen after going to Features or QuickViews > and > clicking the Ligand button to hide the non-standard residues, which by PDB > convention must be designated as HETATM). To see the alpha carbons in > non-standard residues: > > select *.ca and not protein > spacefill 0.6 > > In 1B07 chain C, a nonstandard amino acid is handled a different way. The > backbone atoms are named GLY (hence its alpha carbon is included in the > backbone path for chain C), while the sidechain is HETATM and given the > name PYL. In RasMol 2.6/Chime, this produces (in stick display) a floating > sidechain unconnected to the main chain. The missing bonds, both for the > single-residue HIS "chain" (mentioned in my previous email) and for the > PYL > connection to GLY 5 are specified in LINK records. > > SUGGESTIONS for Jmol > > Perhaps backbone paths should include all alpha carbons and nucleotide P > atoms, regardless of whether the residues are standard? I believe that Jmol does this. Today it will not support 'very non-standard' cases ... like something stuck in the chain that does not have N-CA-C-O along the backbone. If there are specific cases of common 'backbone-substitute-sequences' then we should discuss them separately. > Perhaps LINK > records should be obeyed to produce additional covalent bonds? I do not believe that Jmol is using LINK records today. Please keep your eye out for an example where Jmol is not doing the right thing. Miguel ------------------------------------------------------- The SF.Net email is sponsored by: Beat the post-holiday blues Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
