Hi Shya, this (admittedly cryptic) message usually indicates that the chain sequence does not match any sequences in the alignments you provide. In the current version, the program actually stops with an error message saying that no alignment has been found (for a certain chain), and is hopefully more self-explanatory. If you find no mismatches, could you send me (not the list!) the files in question, and I will investigate. Sculptor tolerates common modifications (e.g. oxidation, glycosylation) to residues, but is not tolerant towards mismatches. One particularly vicious case is seleno-methionine, which is (as a special case) recognized by sculptor as M, but often put down as X in the sequence/alignment file. I am currently in two minds whether this special case should be kept as it creates more confusion than the additional sequence check it provides. Best wishes, Gabor On Apr 10 2010, [email protected] wrote:

Dear all,

I was trying to generate a model using the sculpt program in phenix. when I run it with both alignment file and pdb file I get the following message: Processing PDB... Next model: ''... Next chain 'A'... No matching alignment for chain 'A'; delete PDB output requested Executing design... Everything is deleted; output file empty

Any help with this...

thanks, Shya _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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