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--- modelangelo [2023/02/17 15:30] – created bonnefon
+++ modelangelo [2024/03/08 14:41] (current) – Luc Bonnefond
@@ Line 1: / Line 1: @@
 ModelAngelo is an automatic atomic model building program for cryo-EM maps.
+[[https://github.com/3dem/model-angelo]]
+===== with IGBMC HPC =====
+  * Upload the protein (and DNA/RNA) sequences as separate fasta files, as well as the map.
+  * Check the hand of the map and flip it in ChimeraX (<quote>''volume flip #1''</quote>) if necessary
+  * Log in to the hpc <quote>''ssh <login>@hpc.igbmc.fr''</quote>
+  * Edit the slurm submission script (with <quote>''nano''</quote> for instance):
+<code>
+#!/bin/bash
+################################ Slurm options #################################
+### Job name
+#SBATCH --job-name=model_angelo
+### Limit run time "1-00:00:00"
+#SBATCH --time=10:00:00
+### Requirements
+#SBATCH --partition=lamour-ruff #(or gpu)
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=1
+#SBATCH --mem-per-cpu=40GB
+#SBATCH --gres=gpu:1
+### Email
+#SBATCH --mail-user=username@igbmc.fr
+#SBATCH --mail-type=ALL
+### Output
+#SBATCH --output=/shared/mendel/projects/xxx/cryoem/model_angelo/model-angelo-%j.out
+################################################################################
+echo '########################################'
+echo 'Date:' $(date --iso-8601=seconds)
+echo 'User:' $USER
+echo 'Host:' $HOSTNAME
+echo 'Job Name:' $SLURM_JOB_NAME
+echo 'Job Id:' $SLURM_JOB_ID
+echo 'Directory:' $(pwd)
+echo '########################################'
+# modules loading
+module load model-angelo/1.0.1
+# acces database
+export TORCH_HOME=/shared/genomes/model_angelo_weights/
+#Job command
+model_angelo build -v map.mrc -pf prot.fasta -df dna.fasta -rf rna.fasta -o output
+echo 'Done.'
+echo '########################################'
+echo 'Job finished' $(date --iso-8601=seconds)
+</code>
+Run the script:
+<code>sbatch model_angelo_script.sh</code>
+You will get one email when the job start and a second one when its complete (or crashed). You can also follow it with <quote>''squeue''</quote>
+===== on POLLUX computer =====
+  * Upload the protein (and DNA/RNA) sequences as separate fasta files, as well as the map.
+  * Check the hand of the map and flip it in ChimeraX (<quote>''volume flip #1''</quote>) if necessary
 === Setup ===
@@ Line 19: / Line 77: @@
 Let's say the map's name is <quote>''map.mrc''</quote> and the sequence file is <quote>''sequence.fasta''</quote>. To build your model in a directory named <quote>''output''</quote>, you run:
-<quote>''model_angelo build -v map.mrc -f sequence.fasta -o output''</quote>
+<code>model_angelo build -v map.mrc -pf sequence.fasta -o output</code>
+If you would like to build nucleotides as well, you need to provide the RNA and DNA portions of your sequences in different files like so
+<code>model_angelo build -v map.mrc -pf prot.fasta -df dna.fasta -rf rna.fasta -o output</code>
+If you only have RNA or DNA, you can drop the other input.
 If the output of the program halts before the completion of <quote>''GNN model refinement, round 3 / 3''</quote>, there was a bug that you can see in <quote>''output/model_angelo.log''</quote>. Otherwise, you can find your model in <quote>''output/output.cif''</quote>. The name of the mmCIF file is based on the output folder name, so if you specify, for example, <quote>''-o testing/test/model_building''</quote>, the model will be in <quote>''testing/test/model_building/model_building.cif''</quote>.