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.