On 1/2/10 6:56 AM, Muthiah I wrote: > I am trying to model a hetero dimer protein using modeller and I couldnt > make it up.. > > the error which i was not able to rectify is > "PROTEIN SPECIFIED IN ALIGN CODES WAS NOT FOUND IN THE ALIGNMENT FILE"
It is generally impossible to deduce your error without seeing at least your full log file or an archive of your inputs (not cut-and-paste). Fortunately, you sent me the latter (model.zip) in a separate post. When I run the latest version (9v7) of Modeller on that input file, I see the following warning in the log file:
check_for__W> This file (alignment.ali) appears to be in Rich Text Format; Modeller will probably be unable to read it correctly. To correct this, save it in plain text format (also termed "ANSI encoding" on Windows systems).
You will need to save the alignment file (and all other inputs, such as PDB files) in plain text format, as described in the log file. Modeller will not read Rich Text Format, Word documents, or other file formats.
Ben Webb, Modeller Caretaker