Difference between revisions of "File formats/Export"
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AngelHerraez (talk | contribs) (new section Export/Save files from Jmol) |
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=== MOL format === | === MOL format === | ||
The top line is an example of Jmol output in each atom's line of a MOL file, while the bottom line is the specification by MDL/Symyx: | The top line is an example of Jmol output in each atom's line of a MOL file, while the bottom line is the specification by MDL/Symyx: | ||
| + | 3.6133866 2.2537918 -2.035789 C | ||
xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee | xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee | ||
| − | |||
Some software pieces are more forgiving than others in reading MOLfiles. | Some software pieces are more forgiving than others in reading MOLfiles. | ||
Revision as of 11:06, 16 December 2010
Exporting or saving molecular model files from Jmol
Although Jmol is basically a viewer, it has some limited capabilities to save files for the displayed molecular model (or a subset of it).
writecommand- Pop-up menu
save isosurfacecommand
MOL format
The top line is an example of Jmol output in each atom's line of a MOL file, while the bottom line is the specification by MDL/Symyx:
3.6133866 2.2537918 -2.035789 C xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
Some software pieces are more forgiving than others in reading MOLfiles.
Jmol export can hence be improved in producing this format:
- Shift the position of the coordinates so that the decimal point is at the right place. Reduce the numebr of decimals accordingly.
- Add the trailing zeros that represent extra, optional, data (mass difference, formal charge, etc.).
