Xiang, I would suggest that whatever software you use to produce the ALC files is changed so that it produces MOL files. These have a well documented format specification and will be read by Jmol as well as RasMol. It seems that Alchemy format is rather old (there isn't even a mention of the program at the Tripos website) and there is no documentation about the format details, so it is difficult and unlikely that Jmol will read it.
> * Firstly, I adopted the alchemy format in 3DNA primarily because it is one > of the formats > supported by RasMol. PDB format is also used in 3DNA for atomic > representations, and > the alchemy format is simpler for schematics by specifying each > node/linkage explicitly. MDL MOL format specifies atoms and bonds as well, and you can easily instruct Jmol to render those bonds only. I guess you could even use plain text files making use of the DATA command in Jmol to draw the boxes you need. > * As I mentioned in my previous message, I am "playing tricks" with the > alchemy format Yes, that was clear. But the brief answer is: Jmol does not understand the alc format. > In relation to Jmol, I am hoping Jmol could render such "non-chemistry-based" > alchemy file > properly. In essence, the render just needs to respect the node and linkage > information explicitly > defined in the file: it does not try to be "clever" to deduce some chemistry > from it. Yes, that is perfectly possible. But you need a file format that Jmol understands. Maybe you can use some utility like OpenBabel to convert ALC to MDL files? or http://www.webqc.org/molecularformatsconverter.php ------------------------------------------------------------------------------ SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
