diff --git a/example_3.md b/example_3.md index 94277d9d..d860a345 100644 --- a/example_3.md +++ b/example_3.md @@ -3,15 +3,19 @@ # Aims: Model activation of phosphoinositide 3-kinase by the influenza A virus NS1 protein (PDB: 3L4Q) ## 1st step: compute multiple sequence alignment (MSA) and template features using provided pbd templates (run on CPU) -his complex can not be modeled with vanilla AlphaFold Multimer, since it is a host-pathogen interaction. -Firstly, download sequences of NS1(Uniprot: [P03496](https://www.uniprot.org/uniprotkb/P03496/entry)) andP85B(uniprot:[P23726](https://www.uniprot.org/uniprotkb/P23726/entry)) proteins. +This complex can not be modeled with vanilla AlphaFold Multimer, since it is a host-pathogen interaction. +Firstly, download sequences of NS1(Uniprot: [P03496](https://www.uniprot.org/uniprotkb/P03496/entry)) and P85B(uniprot:[P23726](https://www.uniprot.org/uniprotkb/P23726/entry)) proteins. Then download the multimeric template in either pdb or mmCIF format(PDB: [3L4Q](https://www.rcsb.org/structure/3L4Q)). Create directories named "fastas" and "templates" and put the sequences and pdb/cif files in the corresponding directories. Finally, create a text file with features description (description.csv): ``` -3L4Q_A.fasta, 3L4Q.cif, A -3L4Q_C.fasta, 3L4Q.cif, C +P03496.fasta, 3L4Q.cif, A +P23726.fasta, 3L4Q.cif, C ``` +In this example we refer to the NS1 protein as chain A and to the P85B protein as chain C in multimeric template 3L4Q.cif. + +**Please note**, that your template will be renamed to a PDB code taken from *_entry_id*. If you use a *.pdb file instead of *.cif, AlphaPulldown will first try to parse the PDB code from the file. Then it will check if the filename is 4-letter long. If it is not, it will generate a random 4-letter code and use it instead. +*Please also note, that currently --use_mmseqs2 flag is not supported for this mode.* Now run: ```bash diff --git a/test/test_data/true_multimer/features/RANdom_name1_.7-1_0_B.pkl b/test/test_data/true_multimer/features/RANdom_name1_.7-1_0_B.pkl new file mode 100644 index 00000000..9e0d770d Binary files /dev/null and b/test/test_data/true_multimer/features/RANdom_name1_.7-1_0_B.pkl differ diff --git a/test/test_predict_structure.sh b/test/test_predict_structure.sh index c4e9d3db..349377e0 100755 --- a/test/test_predict_structure.sh +++ b/test/test_predict_structure.sh @@ -42,6 +42,6 @@ MAXRAM=$(echo `ulimit -m` '/ 1024.0'|bc) GPUMEM=`nvidia-smi --query-gpu=memory.total --format=csv,noheader,nounits|tail -1` export XLA_PYTHON_CLIENT_MEM_FRACTION=`echo "scale=3;$MAXRAM / $GPUMEM"|bc` export TF_FORCE_UNIFIED_MEMORY='1' - +echo "Running TestScript::testRun_$SLURM_ARRAY_TASK_ID" pytest -s test/check_predict_structure.py::TestScript::testRun_$SLURM_ARRAY_TASK_ID pytest -s test/check_predict_structure.py::TestFunctions::test_get_$SLURM_ARRAY_TASK_ID \ No newline at end of file