Blastermaster2.0

Installation

System dependencies

You will need CSH to run .csh files.

E.g., on Ubuntu 20:

sudo apt-get install csh

At least some of the blaster programs that BM2 depends on are 32-bit, so if you are installing on a 64-bit architecture then you will need to enable 32-bit architecture and install the relevant libraries

E.g., on Ubuntu 20:

sudo dpkg --add-architecture i386
sudo apt-get update -y
sudo apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386

E.g., on CentOS 7:

yum install glibc.i686 libstdc++.i686

Installing using Pip

Assuming you have a valid GitHub personal access token (PAT) attached to a GitHub account that has read-access to Blastermaster 2.0 repository within the Docking.org GitHub organization, you can install BM2 to a given Python environment using Pip:

pip install https://<GIT_ACCESS_TOKEN>@raw.githubusercontent.com/docking-org/blastermaster-2.0/main/dist/bm2-<SEMANTIC_VERSION>-py3-none-any.whl

where <GIT_ACCESS_TOKEN> and <SEMANTIC_VERSION> are replaced by their corresponding / desired values. E.g. semantic version: 0.1.0

Using Blastermaster 2.0

UCSF Shoichet Lab members

If you are a member of the UCSF Shoichet Lab, you can use BM2 on one of the UCSF computers where it is already set-up. See here: https://wiki.docking.org/index.php/How_to_use_Blastermaster_2.0_on_UCSF_computers

All others

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. Generate a blaster config file to your directory

The following will generate a file called "blasterconfig.yaml"

blasterconfig

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

blasterconfig <BLASTER_CONFIG_FILE_NAME>

3. Crucially, set an environmental variable called `DOCKBASE` to the path of your DOCK software directory.

export DOCKBASE=<PATH_TO_DOCK_REPOSITORY>

3. 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. blasterconfig_default.yaml, blasterconfig_use_existing_charged_receptor.yaml). Then it is easy to reuse the same configuration settings at a later time.