ModelAngelo is an automatic atomic model building program for cryo-EM maps.

References:

• Jamali K., Kimanius D., Scheres SHW. A Graph Neural Network Approach to Automated Model Building in Cryo-EM Maps. International Conference on Learning Representations (2023).

• ModelAngelo Main Site

• Module Name: model-angelo (see the modules page for more information)
• Multithreaded
• GPU dependent

Some features of ModelAngelo require the hhblits command of hhsuite.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --gres=gpu:a100:1 --mem=20g -c 8
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load model-angelo

[user@cn3144 ~]$ model_angelo build -v map.mrc -f sequence.fasta -o output

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. model-angelo.sh). For example:

#!/bin/bash
set -e
module load model-angelo
model_angelo build_no_seq -v map.mrc -o output
hhblits -i output/hmm_profiles/A.hhm -d PATH_TO_DB -o A.hhr -oa3m A.a3m -M first

Submit this job using the Slurm sbatch command.

sbatch --gres=gpu:a100:1 --partition=gpu --mem=20g -c 8 model-angelo.sh