Ok, Raphael, it's solved.
Your protein pdb file is somewhat singular: there are nonstandard
amino acid residues (RET, MSE), ions (HG, ZN, NI, NA), water (HOH)
and sugars (MAN, NAG). But all are marked as ATOM records and have a
residue number, so Jmol sees no HETERO groups, hence no LIGANDS
either.
The nonstandard amino acid residues give no problem (if you need it,
they can be selected as "protein and not amino", or by their resiude
name).
Your problem with trace is due to MAN and NAG being recognized as
monosaccharides ("carbohydrate" keyword). Although this is
undocumented, Jmol draws traces, ribbons etc for carbohidrate
residues (I guess using their C1 atom). And the problem comes because
the numbering of these residues (all of them at the end of the chain)
does not mean sequence, but Jmol is assuming that meaning, so it's
joining them at the end of the protein. That's the big zigzag line
you see.
Simplest solution: draw trace only for protein:
background white;
select all;
wireframe off;
backbone off;
spacefill off;
select protein; // important
trace on;
select :a;
color trace bisque;
select :b;
color trace lightgrey;
select all;
Good luck
-------------------------------------------------------------------------
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
