Re: [modeller_usage] Protein not accepted

Giacomo Bastianelli wrote: > I had to do an automodelling of a protein based > on a template. > > I first ran the seqcheck and use the sequences that I got for the > alignment (using tcoffee). > > I prepared the alignment file as follow: ... > >P1;1WMD > structureX:1WMD: 1 :A: 434 :A:undefined:undefined:-1.00:-1.00 ... > pdbnam__217W> Filename for PDB code not found: 1WMD

Your alignment file says your PDB file is code 1WMD, so Modeller will try file names 1WMD.pdb, 1WMD.atm, pdb1WMD.ent, etc. Remember that Modeller is case sensitive, so it won't read a PDB file called '1wmd.pdb' for example.

Ben Webb, Modeller Caretaker