Alphafold Submit Script Reference

Introduction

This reference contains information on about which variables to change in the AlphaFold Submit script provided by the UFS HPC.

Please note that the line numbers for the variables may be subject to change (as the script might change). They are only provided as a relative guide to locate the relevant variables in the script.

For an explanation of the parameters that are mapped to the variables in this reference, see the Parameter Reference page

Required Variables

Line Number(s)	Variable in script	Alphafold variable	Description
3, 9, 10	{job_name}	-	An appropriate title for the submission
33	FASTA_PATHS	fasta_paths	Path to current file(s).
47	OUTPUT_DIR	output_dir	Directory where output should be created. Path is relative to the directory created in step 2.
82	MODEL_PRESET	model_preset	Prediction model to use
102	IS_PRO_LIST	is_prokaryote_list	For multimer model only. Define whether the source of fasta sequences are of prokaryotic origin

Optional variables

Line Number(s)	Variable in script	Alphafold variable	Description
40	DATA_DIR	data_dir	Path to the directory of supporting data.
58	MAX_TEMPLATE_DATE	max_template_date	Maximum date of structures to consider as templates. Any template added after this date will be ignored. The default is the current date and is automatically set in the script
69	DB_PRESET	db_preset	Preset for the MSA database configuration.
113	USE_PRECOMPUTED_MSAS	use_precomputed_msas	Use precomputed msas files - Please see the note below
114	MSAS_PATH

USE_PRECOMPUTED_MSAS Note:

To use precomputed MSA's do the following:

• Set the value of the USE_PRECOMPUTED_MSAS variable to "yes".
• Next, copy the directory containing the MSA's into a directory inside the directory that contains the submit script and the query fasta files.
• Finally set the MSAS_PATH to the directory in the above step (Do not use the full system path, use the path relative to the working directory). For example: If the MSA directory named msa_done is in the root of the directory with the submit script, the path should be msa_done/