Bob Hanson wrote:
As Miguel suggests and my demo shows, the thing you need to do is to separate
the different models using
MODEL ENDMDL
as shown, for example, at
http://rcsb-deposit.rutgers.edu/adit/docs/pdb_atom_format.html
from the PDB Format Description Version 2.2 http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html
* For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM <http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_67.html> list uses the following general rules:
- In the simple case that involves a few atoms or a few residues
with alternate sites, the coordinates occur one after the other in
the entry.
- In the case of a whole macromolecular chain, or significant
portion of a chain, having alternate sites, the atoms for each
alternate position are listed together. The two conformers are
delineated by MODEL/ENDMDL
<http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_68.html>
records. In this case each MODEL must represent the entire molecular
assemblage, including any heterogen group which is not necessarily
disordered. Such is the case when DNA molecules are placed in UP and
DOWN positions.
- In the case of a large heterogen groups which are disordered, the
atoms for each conformer are listed together. The two lists are not
separated by MODEL/ENDMDL
<http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_68.html> as is
done for macromolecular chains.
it is clear that using column 17 field altLoc an Alternate location indicator would be more appropriate for a single residue rotameres and Jmol had to support this.
We may discuss about the connection around alternative *.CB;A atoms (or other connection atoms to the main model).
The simplest case would be no connection like in MODELs but the better implementation to my opinion would be, that all alternative *.CB;A atoms are connected to the common *.CA
which was visible according to the selection.
...
MODEL 1 ...
Animation scripts should consider the common main model as part of each alternative model *;ATER 295 GLU 18 ENDMDL
Of course the catch is that with this you need to duplicate ALL the entries.
A nice benefit of this is that then you can run the animations and watch your
rotomers interconvert.
With 80+ rotomers that's a BIG file.
such a large number of rotamers is not necessary for a single alternative monomer in a biopolymer, in this case only the MODELs solution might be possible.
Regards, Jan
...
One PARTIAL solution, actually a pretty nice one would be an option in Jmol such as
set interchainbonding ON/OFF
I don't like it, what about chemical cross links, SS bonds, bonds
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