Jmol users interested in using Jmol for more than viewing:
I have added some new command-line options.
What do you think of this? (Using the applicatoin from a Windows command prompt)
Create a JVXL file directly
---------------------------
Jmol -ionx iso.spt myfile.xyz > myfile.jvxl
where:
-i,--silent silent startup operation
-o,--noconsole no console -- all output to sysout
-n,--nodisplay no display (much faster)
-x,--exit run script and exit
iso.spt is:
isosurface solvent;show isosurface
creates a JVXL solvent surface file.
Create a JVXL file directly
---------------------------
Jmol -ionx mo.spt myfile.xyz > myfile.jvxl
where mo.spt is:
mo 12; show mo
creates a JVXL file of the 12th MO.
Create a list of measurements
-----------------------------
Jmol -ionx measure.spt myfile.xyz > measure.txt
where measure.spt is:
measure allconnected (*) (*);show measurements
generates a list of measurements.
measure.txt now contains (tab-separated):
Measurement Information
distance 1.1217928 0.112 nm H 1 #1 C 10 #10
distance 1.4158994 0.142 nm N 2 #2 C 6 #6
distance 1.3865448 0.139 nm N 2 #2 C 7 #7
...
Anything that can be "shown" can be dumped to a file this way.
Check CIF file symmetry
-----------------------
Jmol -ionx symmetry.spt myfile.cif > symmetry.txt
where symmetry.spt is:
show unitcell;show symmetry;show spacegroup;
symmetry.txt now contains:
a=9.8737, b=9.8737, c=2.8518999, alpha=90.0, beta=90.0, gamma=90.0
Symmetry Information:
model #1; name=75539-ICSD
Spacegroup: I 4/m
Number of symmetry operations: 16
Symmetry Operations:
x,y,z
-y,x,-z
y,-x,-z
x,y,-z
-x,-y,-z
y,-x,z
-y,x,z
-x,-y,z
-y+1/2,x+1/2,-z+1/2
y+1/2,-x+1/2,-z+1/2
x+1/2,y+1/2,-z+1/2
-x+1/2,-y+1/2,-z+1/2
y+1/2,-x+1/2,z+1/2
-y+1/2,x+1/2,z+1/2
-x+1/2,-y+1/2,z+1/2
x+1/2,y+1/2,z+1/2
Hermann-Mauguin symbol: I 4/m
international table number: 87
Hall symbol: -I 4
primitive Hall symbol: P 4z 1n -1
lattice type: -I: centrosymmetric body-centered
rotation term 1
input code: 4; primitive code: 4z
order: 4; axisType: z
operator: -y,x,z
Seitz matrix:
{ 0 -1 0 0 }
{ 1 0 0 0 }
{ 0 0 1 0 }
{ 0 0 0 1 }
etc., etc.
Here's a list of the SHOW command options that might be of particular
interest:
show file
show isosurface
show measurements
show mo
show model
show pdbheader
show spacegroup
show symmetry
show unitcell
oh, and anything you can get from getProperty will do the same:
getProperty fileContents
------------------------
getproperty fileContents "http://www.rcsb.org/pdb/files/1DPO.pdb";
saves 1DPO.pdb on your hard drive.
getProperty auxiliaryInfo
-------------------------
auxiliaryinfo {
someModelsHaveFractionalCoordinates true,
someModelsHaveSymmetry true,
someModelsHaveUnitcells true,
models [{
symmetryOperations
["x,y,z","-y,x,-z","y,-x,-z","x,y,-z","-x,-y,-z","y,-x,z","-y,x,z","-x,-y,z","-y+1/2,x+1/2,-z+1/2","y+1/2,-x+1/2,-z+1/2","x+1/2,y+1/2,-z+1/2","-x+1/2,-y+1/2,-z+1/2","y+1/2,-x+1/2,z+1/2","-y+1/2,x+1/2,z+1/2","-x+1/2,-y+1/2,z+1/2","x+1/2,y+1/2,z+1/2"],
structuralFormula "(N H4) Mn8 O16",
symmetryCount 16,
presymmetryAtomCount 4,
presymmetryAtomIndex 0,
formula "H4 Mn8 N1 O16",
notionalUnitcell
[9.8737,9.8737,2.8518999,90.0,90.0,90.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN],
spaceGroup "I 4/m",
chemicalName "Ammonium manganese oxide (1/8/16)",
coordinatesAreFractional true,
latticeDesignation ""
}]
}
getProperty atomInfo
--------------------
element "hydrogen"
visible true
model 1
radius 0.5
visibilityFlags 13
clickabilityFlags 12
bondCount 1
atomno 1
elemno 1
z 0.0
y 0.0
x 2.4571667
You get the idea. I just uploaded the code; coming in 10.9.66; suggestions?
Bob
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