Hello,

I am just starting to use Modeller. Even though I have a major in computer science, have used many bioinformatics tools, and am familiar with Python, I haven't been able to figure out how to run this program. To be honest I don't find it that user-friendly! Basically I'm not sure in which folder I have to put my alignment and PDB coordinate files. This is the alignment file that I have created but am not sure if it meets the specifications (they both refer to HIV-1 protease, residues 1 to 99 of chain A);

P1;1A8GA

structureX:1A8GA:1:A 99:A:.:.:.:. PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*

P1;1ZPA

sequence:1ZPA:1:A 99:A:.:.:.:. PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF*

The error message that I'm getting is "Structure not read in: 1" and it's raised from the Modeller8v1\modlib\modeller\util\top.py file.

I would appreciate your help on this. Omid K.