Hi Bob,
Trying out the new commands on
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
and I am getting errors such as
script compiler ERROR: command expected
----
>>>> file 0 <<<<
and
script ERROR: java.io.FileNotFoundException: http://www.stolaf.edu/
academics/chemapps/jmol/docs/examples-11/data/cholesterol.mol
----
load >> "cholesterol.mol" <<
Frieda
On Feb 14, 2007, at 7:01 PM, Bob Hanson wrote:
I have just checked in a version of Jmol that allows:
inverting selected atoms about points and planes
writing of selected coordinates and orientation
reading those files back into Jmol
Basically, there is a new command:
invertSelection
which by itself inverts all atoms through the center of rotation
invertSelection POINT [some point description]
which inverts selected atoms through a point
invertSelection PLANE [some plane description]
which inverts selected atoms across a plane
Now, once this is done, of course, the atoms are not where they
used to
be. That would mess up the state, so I have added a new DATA type
called
"coord":
DATA "coord set"
24 ;
Jmol Coordinate Data Format 1 -- Jmol 11.1.13 2007-02-14 15:54;
1 H H1_#1 2.9400268 2.3187106 -0.35901633 ;
2 N N2_#2 -1.4280989 2.2970076 0.9680812 ;
3 C C3_#3 -0.5195322 0.37288004 -0.24890617 ;
...
24 H H24_#24 0.7507625 -1.5374694 -1.5575587 ;
end "coord set";
which allows setting of atom coordinates in bulk. This is
necessary, of
course, because if you move the atoms, we have to reproduce that in
the
script.
So with that, it seemed simple enough (about 10 lines of code) to
create:
write coords
which writes the same SPT script as
write state
except it also includes coordinate positions.
SO, having done that, it seemed ridiculous if Jmol could write
coordinates but not read what it had written, so I added a tiny
JmolDataReader to read those files.
I really don't know if that is of any particular use. But it was
simple
enough to do.
But more useful, probably, would be the ability to write the
coordinates
in a more standard format, and if people feel strongly that we should
NOT be able to read these script files this way, I would be happy to
remove that capability.
Comments? Suggestions for perhaps a SIMPLE general format for writing
coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited,
but with bonds), PDB? (unlimited, but rather involved).
Alternatively, should Jmol have a new "native format" that includes
the
"state"?
I don't want to make a big deal about this; just wondering.
And, yes, I know -- the next thing needed is "rotateSelected". I'm
working on that. When that is in, we can start having quite some fun
with loading two files, inverting one, moving it above the other,
rotating it independently, etc. I think there might be some nice
applications that would use this capability.
Bob
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Frieda Reichsman, PhD
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
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