>I'm trying to model another protein (HSP) and I'm having trouble again. >Please look the second line of my alignment file >structureX:1uy7:2:A:236:A:::-1.00:-1.00

Dear Elton, I have seen your log messages and downloaded the pdb file to test it on my PC. It seems that you have the same problem I had some time ago. The problem appears when there are missing atoms in the structure. If you see the REMARKS section at the pdb file you will get a complete list of missing atoms in the model. You have to delete these from the alignment files, so modeller can match the residues in the alignment with the ones in the pdb file. Replace the missing residues with gaps in the alignment and you will be able to continue with your work. You have to note also that you will have to modify the second line of the alignment since the first residue in the structure is 16:A, not 2A. I hope you solve your problem.

Best regards, Cesar Avila Universidad Nacional de Tucuman Argentina

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