Ah, OK. That's it. Thanks, Rolf.
Dwey, try wrapping your structure data with
load DATA "mydata"
...
end "mydata"
and then use the Jmol -s - option.
-s indicates to read a script file, and "-" indicates that we are using
System.in for that file data.
>From jmol -h:
-s,--script <arg> script file to execute or '-' for
System.in
That is sure to work.
My perl is quite rusty, but it may be as simple as:
cat pdb1deh.ent | perl -ne 'BEGIN { print "load DATA \"mydata\"\n";} END {
print "END \"mydata\"\n";}' | java -jar Jmol.jar -s -
Bob
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