How to use Blastermaster 2.0 on UCSF computers: Difference between revisions
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= Using Blastermaster 2.0 = | = Using Blastermaster 2.0 = | ||
== 0. Copy the | == 0. Copy the relevant input files 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. If you want to provide your own rec.crg.pdb, copy that in too. Blastermaster 2.0 will look for these in the directory in which you run it (or at whichever file paths you set for their corresponding parameters in the config file). | ||
== 1. Source the relevant pre-configured environment == | == 1. Source the relevant pre-configured environment == | ||
Gimel: | |||
source /nfs/ | === Gimel === | ||
Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like: | |||
/lib64/libc.so.6: version `GLIBC_2.15' not found | |||
Source a Python environment | |||
source /nfs/soft/ian/python<PYTHON_VERSION>.sh | |||
where <PYTHON_VERSION> is replaced with one of the available python versions. E.g.: | |||
source /nfs/soft/ian/python3.8.5.sh | |||
To check which python versions are available, run | |||
ls /nfs/soft/ian/python*.sh | |||
== 2. Generate a blaster config file to your directory == | == 2. Generate a blaster config file to your directory == | ||
The following will generate a file called " | The following will generate a file called "blasterconfig.yaml" | ||
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> | ||
| Line 17: | Line 29: | ||
== 3. Edit the blaster config file to your specifications == | == 3. Edit the blaster config file to your specifications == | ||
The parameters in the config file govern the behavior of blastermaster. | |||
To enter the vi text editor: | To enter the vi text editor: | ||
| Line 29: | Line 42: | ||
Press "x!" followed by "RETURN" to save your edits and exit the text editor. | Press "x!" followed by "RETURN" to save your edits and exit the text editor. | ||
== 4. Run == | == 4. Run == | ||
blastermaster < | If you used the default blaster config file name, then you can simply run: | ||
blastermaster | |||
Otherwise: | |||
blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH> | |||
If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows: | |||
blastermaster --charged_receptor_file_path=<PATH_TO_FILE> | |||
= Tips for users = | = Tips for users = | ||
You can create and save multiple blaster config files with different settings so long as they have different names (e.g. | 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_elec_only_thinspheres.yaml). Then it is easy to reuse the same configuration settings at a later time. | ||
Latest revision as of 19:31, 7 June 2022
Using Blastermaster 2.0
0. Copy the relevant input files to your directory
Copy your rec.pdb and xtal-lig.pdb files to your directory. If you want to provide your own rec.crg.pdb, copy that in too. Blastermaster 2.0 will look for these in the directory in which you run it (or at whichever file paths you set for their corresponding parameters in the config file).
1. Source the relevant pre-configured environment
Gimel
Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like:
/lib64/libc.so.6: version `GLIBC_2.15' not found
Source a Python environment
source /nfs/soft/ian/python<PYTHON_VERSION>.sh
where <PYTHON_VERSION> is replaced with one of the available python versions. E.g.:
source /nfs/soft/ian/python3.8.5.sh
To check which python versions are available, run
ls /nfs/soft/ian/python*.sh
2. 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. Edit the blaster config file to your specifications
The parameters in the config file govern the behavior of blastermaster.
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
If you used the default blaster config file name, then you can simply run:
blastermaster
Otherwise:
blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>
If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:
blastermaster --charged_receptor_file_path=<PATH_TO_FILE>
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_elec_only_thinspheres.yaml). Then it is easy to reuse the same configuration settings at a later time.