Bob Hanson wrote: > [EMAIL PROTECTED] wrote: > >> Quoting Angel Herraez <[EMAIL PROTECTED]>: >> >> >> >>> On 15 Oct 2007 at 19:21, Rolf Huehne wrote: >>> >>> >>>> 5) You have to be careful with hetero component residue names. They >>>> might clash with reserved words in Jmol. Therefore we avoid including >>>> the residue name in the set definition. >>>> >>>> >>> The safe way is to enclose residue names in square brackets. That's >>> required or at least >>> highly recommended when the residue name has numbers (such as SO4) , >>> but it's safe in all >>> cases. >>> >>> >> It's not safe in all cases. I don't remember the exact cases but there >> were quite a lot of hetero residue names that were rejected by Jmol >> even in square brackets. >> When I reported the problem quite a while ago on this list, Miguel >> told that it would require a major rewrite of the command parser and >> this would not happen soon. >> I havn't checked this systematically since then, but I don't expect >> that they will work now. >> >> >> > That major rewrite was done; brackets work for any name. Correct me if I > am wrong.... >
You are wrong. I tested some problematic cases with Jmol 11.3.33 Revision 8438 (build from SVN) and they are still problematic: "SET", "2MO": select [SET]17:A; select [2MO]17:A; I wanted to analyze this systematically using the command-line syntax check option. But it was quite useless. Each scriptfile contained a single command as in the examples above and Jmol was started using the following command-line: java -jar Jmol.jar -n -c -s scriptfilename The output was not very informative. In most cases there was only the following message (1 or 2 times): --checking script: null ---- Sometimes there was additionally the following kind of message: select [118]17:A; --script check ok The "null" message was there for "2MO" but also for a lot of others that worked fine if invoked manually. So I can't provide you with a complete list of problematic cases. In general the behaviour of Jmol in command-line mode is not very unix-like: 1) Usually the output is send to "STDOUT" and the error or log messages are send to "STDERR". This allows for an easy separation of real output and other messages and simplifies output parsing. So I would expect that something like "syntax ok" or "syntax not ok" would be the output with the command-line switch "-c". 2) The silent option unfortunately (and unexpectedly) makes Jmol totally silent. Usually such an option is used to suppress any commenting or warning messages but not the requested output. Regards, Rolf ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
