Bob Hanson wrote:
...
I use callbacks in RasMol to query e.g. which amino acids are in 3.2
A distance to a hetero component
(echo "load pdb inline\nselect within(3.2, [LIP]3) and not
[LIP]3\nshow selected group\nexit\n";cut 1imb.pdb) | rasmol
-nodisplay | evaluateMakeRasMolScriptFromIt.pl | rasmol
without any user, the startup JmolScript could replace the
interacting user, that is the main use for messageCallback
Ah, I see. OK. Well, it's an interesting question how to do:
PDB FILE | (cut off a chunck) | (do something with it) | Jmol
PDB FILE | (extract some information form it, e.g. ligands of a hetero
component, and generate a script to visualize) | Jmol or RasMol or Chime
that is what already runes using (rasmol -nodisplay) to extract e.g.
ligand information,
rasmol with the -nodisplay option has the flexibility to be used as a
simple automatic script driven structure analysis tool
but
I don't know how Jmol is set up for command-line work like this. It
hardly seems like it would be necessary to run Jmol twice (like you
are running rasmol twice). Maybe this is a nice use for rasmol instead
of Jmol. It does work there --- so why Jmol?
with the Jmol applet, web server side processing isn't necessary any
more, the idea is, that all the automatic structure analysis could be
done on client side while a startup JmolScript is running and a
structure specific visualization script is generate, which completes the
start process (generating structure specific interaction panels ...).
(
at this time I'm sad that both, RasMol and Jmol didn't support the PDB
format completely e.g. ^insCode versus ;altLoc
but I count on you and Jmol which is evolving and will make it some day,
and is relay a great applet.
)
Regards, Jan
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