I'm trying to generate the input files for membrane ab-initio. I already created the span file using OCTOPUS.
However, the run_lips.pl script keeps failing. It creates blast outputs (blast and blast.msa files) but the raw file is empty and the lips4 file contains only the header, and the lipo file is also without values.
I think there's some problem with the part running this script- "http://gila.bioengr.uic.edu/cgi-bin/lips/script.cgi".
Can anyone help me with that?
I think the host changed the web address 'gila.bioe' instead of 'gila.bioengr'
Almost there - trying gila.bioe sends you to http://tanto.bioengr.uic.edu/lips/ which results in an error, but change that to http://tanto.bioe.uic.edu/lips/ and you get a webpage.
I think (but have not tested) that changing the url at line 107 or so in the run_lips.pl script to "http://tanto.bioe.uic.edu/lips/lips.txt" should fix things.
I've just hit this problem myself. The solution suggested in #3 won't work as the url isn't run as a cgi script, it's just where the script can be downloaded from.
However, if the script is downloaded (from: http://tanto.bioe.uic.edu/lips/lips.txt) and made executable and the run_lips.pl is made to point at the script rather then the url, so that the script is run locally, things work fine.
As the script is made freely available and there appears to be no licence associated with it, could it not be included in the Rosetta distribution in order to prevent other users stumbling over this? Unfortunately there currently isn't even an error message to indicate that something has gone wrong, so users won't realise that they aren't using the optimal pipeline.
I faced the same problem with the cgi script. How exactly did you change the run_lips.pl to get it to work with the downloaded txt file?
If you've downloaded our script as (e.g.) /home/you/rosetta/lips.txt, you first need to make it executable with the command:
chmod +x /home/you/rosetta/lips.txt
Then edit run_lips.pl and change (roughly) line 132 from:
Hope that helps.