14fb4111cf84320105cc68b9e8d203f43f9bc7b7
downloads/alphafold_monomer_2.1.2.sh
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1 | +#!/bin/bash |
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2 | + |
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3 | +input=$1 |
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4 | + |
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5 | +ALPHAFOLD_X=2.1.2 |
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6 | +/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \ |
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7 | + --data_dir=/programs/local/alphafold/ \ |
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8 | + --output_dir=$(pwd) \ |
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9 | + --fasta_paths=${input} \ |
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10 | + --max_template_date=2020-05-14 \ |
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11 | + --db_preset=full_dbs \ |
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12 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
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13 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
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14 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
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15 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
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16 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
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17 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
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18 | + --use_gpu_relax=True \ |
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19 | + --model_preset=monomer \ |
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20 | + --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
downloads/alphafold_multimer_2.1.2.sh
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1 | +#!/bin/bash |
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2 | + |
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3 | +input=$1 |
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4 | + |
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5 | +ALPHAFOLD_X=2.1.2 |
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6 | +/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
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7 | + --data_dir=/programs/local/alphafold \ |
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8 | + --output_dir=$(pwd) \ |
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9 | + --fasta_paths=${input} \ |
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10 | + --max_template_date=2020-05-14 \ |
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11 | + --db_preset=full_dbs \ |
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12 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
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13 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
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14 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
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15 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
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16 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
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17 | + --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
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18 | + --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
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19 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
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20 | + --use_gpu_relax=True \ |
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21 | + --model_preset=multimer |
examples/alphafold2.md
... | ... | @@ -158,7 +158,7 @@ Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`, |
158 | 158 | --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 |
159 | 159 | ``` |
160 | 160 | |
161 | -where test_monomer.fasta is |
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161 | +where the input fasta is |
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162 | 162 | |
163 | 163 | ``` |
164 | 164 | >T1083 |
... | ... | @@ -185,7 +185,7 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA |
185 | 185 | --model_preset=multimer |
186 | 186 | ``` |
187 | 187 | |
188 | -where test_multimer.fasta is |
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188 | +where the input multimer fasta is |
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189 | 189 | |
190 | 190 | ``` |
191 | 191 | >T1083 |
... | ... | @@ -194,6 +194,12 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA |
194 | 194 | MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |
195 | 195 | ``` |
196 | 196 | |
197 | +You can download example scripts of the above here: |
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198 | +[alphafold_monomer_2.1.2.sh](downloads/alphafold_monomer_2.1.2.sh) |
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199 | +[alphafold_multimer_2.1.2.sh](downloads/alphafold_multimer_2.1.2.sh) |
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200 | + |
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201 | + |
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202 | + |
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197 | 203 | **Alphafold2 2.1.1** |
198 | 204 | **Standard prediction example :** |
199 | 205 | ``` |