Difference between revisions of "File formats"

Latest revision as of 22:56, 26 January 2020

Jmol + JSmol Documentation

Description of files in Jmol+JSmol distribution
File formats read or written by Jmol
The Jmol scripting interface
- Scripting as a programming language
- Complete reference of scripting commands:
  - at St Olaf (primary site)
  - at Jena3D (mirror)
Loading models directly from databases
Mouse manual
Default colors used by Jmol
Atom sets predefined in Jmol
Support for bond orders · isotopes · stereochemistry · hydrogen bonds
Jmol as editor
Multi-touch support
Copying and pasting state scripts between applets.
Backward compatibility (changes of behavior across versions)
Features added since version 10
Users mailing list (and a mirror)

(An attempt to compile information on file format specifications. It's not complete yet.)

Jmol example/test data files in all formats accepted.

File formats on Open Babel.

Nice description of 3D Geometry & Modeling Formats by Wolfram Mathematica.

See the specific subsections:

File Formats

@@ Line 1: / Line 1: @@
-(A timid attempt to compile information on file format specifications. Far from complete yet.)
+{{Jmol_Documentation_Sections}}
+(An attempt to compile information on file format specifications. It's not complete yet.)
-= (Gaussian) Cube format =
+Jmol [{{SVN Trunk}}Jmol-datafiles/ example/test data files] in all formats accepted.
-Original from Gaussian software ([http://www.gaussian.com/ Gaussian website]).
-Description of Cube Input and Cube Output formats:
+[[:en:Chemical_file_format|Chemical file formats]] on Wikipedia.
-http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
+[http://openbabel.sourceforge.net/wiki/Category:Formats File formats] on Open Babel.
-= MOL format =
+Nice description of [http://reference.wolfram.com/mathematica/guide/3DGeometryAndModelingFormats.html 3D Geometry & Modeling Formats] by Wolfram Mathematica.
-Original from Elsevier MDL.
-Official document: http://www.mdl.com/downloads/public/ctfile/ctfile.pdf
+See the specific subsections:
+<div style="width:30ex;">
+{{File_Formats}}
-= PDB format =
+</div>
-(Official Protein Data Bank document) Atomic Coordinate Entry Format Description:
+<div style="clear:both;"></div>
-http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html