Different alphafold version  get  different results
@lamyankin 
When you run the multimer system you use 5 different models and, possibly, 5 different runs for each model (each one with a different seed).
To make sure you are comparing the same results you need to check the model name and seed used to run the inference.

There are v3 (from v2.3.0) and v2 (from v2.x.x) models.
I did some tests and the v3 performs much better.



I run the alphafold in different version（one is v2.2.4, another is earlier ）and get  different results using the model_preset of multimer. As shown in the picture:

![image](https://user-images.githubusercontent.com/86952016/208279985-109332b8-a8ed-41ac-b1a5-893f86c737d0.png)

This is a complex composed of Cas9 and SNRPD2 (red)  proteins. The predicted struture of cas9 is nearly the same in both results, as well as SNRPD2. However, the binding site of the cas9 and SNRPD2 is different in two results. 

I want to know if it's because of the different versions of alphafold or because of my command?
here is my command:
nohup python3 docker/run_docker.py \
 --fasta_paths=/home/zwf/alphafold/hpl1.fasta,/home/zwf/alphafold/SNRPD2.fasta \
 --model_preset=multimer \
 --docker_user=0 \
 --db_preset=full_dbs \
 --output_dir=/data/alphafold_outdir \
 --max_template_date=2021-12-10 \
 --data_dir=/data/alphalfold &> /home/zwf/alphafold/SNRPD2.out&