Modeller protokoll BCKDHA

To get Modeller started, we first had to create a few starting files.

For each of our template sequences 1w85 and 2r8o we had to create a pairwise alignment with our target sequence 1u5b. This pairwise alignment should be in the modeller PIR format. The alignment files were obtained by JALVIEW through the following procedure:

• Go to > Tools > Preferences > Output. Check if "PIR" output format and "Use Modeller Output" are activated.
• Go to File > Fetch Sequences and select the PDB database. To retrieve a pairwise alignment, enter the corresponding two pdb entries in the field and seperate them by a semi colon. If you want to specify a specific chain insert the pdb id and the chain, seperated by a colon.
  Example: 1UB5:A;1W85:A
• The generated alignment can be downloaded as in PIR format.

Modeller takes an py-file which specifies the sequences and alignment file to be used. The model-default.py can be found in /apps/modeller9.9/examples/automodel. Here we changed 'alignment.ali' to 1w85_1u5b.pir, knowns = '1W85' (our first target) and sequence = '1U5B' (out template). The file was saved as model1w85.py

Make sure to provide the PDB coordinate files in the folder /atom-files.

Modeller is executed by the following command: mod9.9 model1w85.py