How to use Blastermaster 2.0 on UCSF computers

Using Blastermaster 2.0

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 relevant pre-configured environment

Gimel:

source /nfs/soft2/ian/env.sh

Wynton: N/A

2. Generate a blaster config file to your directory

The following will generate a file called "blaster_config.ini"

blasterconfig

The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME>

blasterconfig <BLASTER_CONFIG_FILE_NAME>

3. Edit the blaster config file to your specifications

Crucially, set the `dockbase` parameter to the path of your DOCK software directory.

To enter the vi text editor:

vi <BLASTER_CONFIG_FILE_NAME>

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

blastermaster <BLASTER_CONFIG_FILE_NAME>

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.