Blastermaster2.0: Difference between revisions
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= Installation = | |||
Assuming you have a valid [https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token GitHub personal access token (PAT)] attached to a GitHub account that has read-access to [https://github.com/docking-org/blastermaster-2.0 Blastermaster 2.0 repository within the Docking.org GitHub organization], you can install BM2 to a given Python environment using Pip: | Assuming you have a valid [https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token GitHub personal access token (PAT)] attached to a GitHub account that has read-access to [https://github.com/docking-org/blastermaster-2.0 Blastermaster 2.0 repository within the Docking.org GitHub organization], you can install BM2 to a given Python environment using Pip: | ||
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sudo apt install libc6:i386 libncurses5:i386 libstdc++6:i386 | sudo apt install libc6:i386 libncurses5:i386 libstdc++6:i386 | ||
== | = 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: [[How_to_use_Blastermaster_2.0_on_UCSF_computers|https://wiki.docking.org/index.php/How_to_use_Blastermaster_2.0_on_UCSF_computers]] | 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: [[How_to_use_Blastermaster_2.0_on_UCSF_computers|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 == | === 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. | 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 == | === 1. Generate a blaster config file to your directory === | ||
The following will generate a file called "blaster_config.ini" | The following will generate a file called "blaster_config.ini" | ||
blasterconfig | blasterconfig | ||
The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME> | The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME> | ||
blasterconfig <BLASTER_CONFIG_FILE_NAME> | blasterconfig <BLASTER_CONFIG_FILE_NAME> | ||
== 2. Edit the blaster config file to your specifications == | === 2. Edit the blaster config file to your specifications === | ||
== 3. Run BM2 == | === 3. Run BM2 === | ||
blastermaster <BLASTER_CONFIG_FILE_NAME> | blastermaster <BLASTER_CONFIG_FILE_NAME> | ||
Revision as of 07:06, 16 March 2022
Installation
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/bm2-0.1.0-py3-none-any.whl
Note: 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 add the 32-bit architecture and install the relevant libraries:
sudo dpkg --add-architecture i386 sudo apt update -y sudo apt install libc6:i386 libncurses5:i386 libstdc++6:i386
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 "blaster_config.ini"
blasterconfig
The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME>
blasterconfig <BLASTER_CONFIG_FILE_NAME>
2. Edit the blaster config file to your specifications
3. Run BM2
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.