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Hello Christos,

you will find the information you seek at http://salilab.org/modeller/manual/node83.html#alignmentformat , and an example from the user-list: http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modelle r_usage.archive.02/Author/article-437.html

For short, 2:@:386:@ means: number_first_aminoacid_in_pdb_file:name_of_chain:last_aminoacid:name_of_ chain, so if your structure has the first 10 aminoacids missing, the last aminoacid available is numbered 432, and the chain is named "B" in the pdb-file, then this should be 11:B:432:B .

Best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz

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