File formats/Compressed
Jmol can read and write (export) a number of compressed file (collection) formats. Two of these are particularly useful.
JMOL
JMOL files, typically with the .jmol extension, are a compressed Zip format containing the structure data file, script file containing the state together with any other necessary files.
The JMOL format can be be exported from J(S)mol using the script command:
write ZIPALL "fileName"
or
write JMOL "fileName"
or from the J(S)mol pop-up menu:
File > Save > Save all as JMOL file (zip)
PNGJ
PNGJ files, typically with the .png extension, are a ZIP extension of the PNG image format containing, in addition to a snapshot image, the structure data file, script file containing the state together with any other necessary files. In other words, PNGJ is a PNG image with JMOL file appended (PNG+JMOL image).
The PNGJ format is particularly convenient in that most operating system and web application file systems will display the png snapshot e.g as an icon or thumbnail image for an email or forum posting attachment. JSmol itself can use the PNGJ format to display a cover image prior to loading the interactive structure.
Since 2011, when the ability to write PNGJ format was introduced with the release Jmol 12.3.7, PNGJ has become the de facto standard file format or many J(S)mol users.
The PNGJ format can be exported from J(S)mol using the script command:
write IMAGE width height PNGJ n "fileName"
The width and height are optional and default to the current frame size.
The amount of compression, n, is a number between 0 and 10 (default 2).
or from the J(S)mol pop-up menu:
File > Export > Export PNG+JMOL image
