[phenixbb] Sculptor

Marie Elizabeth Fraser frasm at ucalgary.ca
Sun Sep 7 17:22:32 PDT 2014

   I'm running Sculptor from the Phenix GUI, trying to improve a molecular replacement model.  I've given the pdb file and a sequence alignment.  Sculptor does not appear to accept the first residues aligned in the sequence alignment.  In the alignment, these residues are residue numbers 42 to 60, so they are on the second line of the fasta file (the first line after the title) and Sculptor starts at residue 61 (the subsequent line).  Residues 42 to 60 of the target are to match the first residues of the pdb model, so in the alignment, there are 41 dashes before the beginning of the sequence for the pdb file.  Am I giving an incorrectly formatted sequence alignment, misinterpreting what Sculptor does or is Sculptor supposed to do this?
   Thank you,   Marie
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