83d0e2f7f829de5ae609de85c3c1d4122eb2110d
downloads/alphafold_monomer_2.1.2.sh
| ... | ... | @@ -1,20 +0,0 @@ |
| 1 | -#!/bin/bash |
|
| 2 | - |
|
| 3 | -input=$1 |
|
| 4 | - |
|
| 5 | -ALPHAFOLD_X=2.1.2 |
|
| 6 | -/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \ |
|
| 7 | - --data_dir=/programs/local/alphafold/ \ |
|
| 8 | - --output_dir=$(pwd) \ |
|
| 9 | - --fasta_paths=${input} \ |
|
| 10 | - --max_template_date=2020-05-14 \ |
|
| 11 | - --db_preset=full_dbs \ |
|
| 12 | - --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
| 13 | - --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
| 14 | - --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
| 15 | - --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
| 16 | - --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
| 17 | - --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
| 18 | - --use_gpu_relax=True \ |
|
| 19 | - --model_preset=monomer \ |
|
| 20 | - --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
downloads/alphafold_multimer_2.1.2.sh
| ... | ... | @@ -1,21 +0,0 @@ |
| 1 | -#!/bin/bash |
|
| 2 | - |
|
| 3 | -input=$1 |
|
| 4 | - |
|
| 5 | -ALPHAFOLD_X=2.1.2 |
|
| 6 | -/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
|
| 7 | - --data_dir=/programs/local/alphafold \ |
|
| 8 | - --output_dir=$(pwd) \ |
|
| 9 | - --fasta_paths=${input} \ |
|
| 10 | - --max_template_date=2020-05-14 \ |
|
| 11 | - --db_preset=full_dbs \ |
|
| 12 | - --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
| 13 | - --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
| 14 | - --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
| 15 | - --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
| 16 | - --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
| 17 | - --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
|
| 18 | - --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
| 19 | - --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
| 20 | - --use_gpu_relax=True \ |
|
| 21 | - --model_preset=multimer |
examples/alphafold2.md
| ... | ... | @@ -195,8 +195,8 @@ MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |
| 195 | 195 | ``` |
| 196 | 196 | |
| 197 | 197 | You can download example scripts of the above here: |
| 198 | -[alphafold_monomer_2.1.2.sh](downloads/alphafold_monomer_2.1.2.sh) |
|
| 199 | -[alphafold_multimer_2.1.2.sh](downloads/alphafold_multimer_2.1.2.sh) |
|
| 198 | +[alphafold_monomer_2.1.2.sh](alphafold_monomer_2.1.2.sh) |
|
| 199 | +[alphafold_multimer_2.1.2.sh](alphafold_multimer_2.1.2.sh) |
|
| 200 | 200 | |
| 201 | 201 | |
| 202 | 202 |
examples/alphafold_monomer_2.1.2.sh
| ... | ... | @@ -0,0 +1,20 @@ |
| 1 | +#!/bin/bash |
|
| 2 | + |
|
| 3 | +input=$1 |
|
| 4 | + |
|
| 5 | +ALPHAFOLD_X=2.1.2 |
|
| 6 | +/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \ |
|
| 7 | + --data_dir=/programs/local/alphafold/ \ |
|
| 8 | + --output_dir=$(pwd) \ |
|
| 9 | + --fasta_paths=${input} \ |
|
| 10 | + --max_template_date=2020-05-14 \ |
|
| 11 | + --db_preset=full_dbs \ |
|
| 12 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
| 13 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
| 14 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
| 15 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
| 16 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
| 17 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
| 18 | + --use_gpu_relax=True \ |
|
| 19 | + --model_preset=monomer \ |
|
| 20 | + --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
examples/alphafold_multimer_2.1.2.sh
| ... | ... | @@ -0,0 +1,21 @@ |
| 1 | +#!/bin/bash |
|
| 2 | + |
|
| 3 | +input=$1 |
|
| 4 | + |
|
| 5 | +ALPHAFOLD_X=2.1.2 |
|
| 6 | +/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
|
| 7 | + --data_dir=/programs/local/alphafold \ |
|
| 8 | + --output_dir=$(pwd) \ |
|
| 9 | + --fasta_paths=${input} \ |
|
| 10 | + --max_template_date=2020-05-14 \ |
|
| 11 | + --db_preset=full_dbs \ |
|
| 12 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
| 13 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
| 14 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
| 15 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
| 16 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
| 17 | + --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
|
| 18 | + --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
| 19 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
| 20 | + --use_gpu_relax=True \ |
|
| 21 | + --model_preset=multimer |