Difference between revisions of "Modeller protocol BCKDHA"
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+ | Modeller can also be called with more than one template. A description how this is done can be found here:[http://salilab.org/modeller/tutorial/advanced.html] |
Revision as of 16:15, 7 June 2011
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 (for more information see [1])
Make sure to provide the PDB coordinate files in the folder /atom-files.
Modeller is executed by the following command:
mod9.9 model1w85.py
Modeller can also be called with more than one template. A description how this is done can be found here:[2]