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.
- 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: