How to use Blastermaster 2.0 on UCSF computers

0. Copy the blaster config file to your directory

Copy your rec.pdb and xtal-lig.pdb files to your directory. Blastermaster 2.0 will look for these in the directory in which you run it.

1. Source the BM2 environment

source /nfs/soft2/ian/env.sh

2. Copy the BM2 config file to your directory

cp $BM2_PATH/blaster_config.ini .

3. Edit the BM2 config file to your specifications

vi blaster_config.ini 

To enter edit-mode, press "i".

Make your edits.

When you're done, press "ESC" to exit edit-mode.

Press "x!" followed by "RETURN" to save your edits and exit the text editor.

4. Run BM2

blastermaster blaster_config.ini

Tips for users

You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blaster_config_default.ini, blaster_config_add_no_hydrogens.ini). Then it is easy to reuse the same configuration settings at a later time.