3f757202ec36552162fd89341f08e30dc3e541fa
examples/alphafold2.md
... | ... | @@ -8,7 +8,8 @@ |
8 | 8 | - [GPU Memory](#gpu-memory) |
9 | 9 | - [Web portal](#web-portal) |
10 | 10 | - [Changes in AlphaFold 2.1.1 multimer](#changes-in-alphafold-211-multimer) |
11 | - - [Examples](#examples) |
|
11 | + - [Examples - Alphafold2 2.1.2](#examples---alphafold2-212) |
|
12 | + - [Examples - Alphafold2 2.1.1](#examples---alphafold2-211) |
|
12 | 13 | - [Known issues](#known-issues) |
13 | 14 | |
14 | 15 | <!-- /TOC --> |
... | ... | @@ -126,22 +127,83 @@ This is the standard SBGrid version override method. |
126 | 127 | |
127 | 128 | Some command line flags have changed since version 2.0.0. We recommend running the `run_alphafold.py` command directly and are not providing a wrapper script ( as we did for 2.0.0) at the present time. |
128 | 129 | |
129 | -### Examples |
|
130 | + |
|
131 | +### Examples - Alphafold2 2.1.2 |
|
132 | +**NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specifed**. |
|
133 | +You can also resume from a previously run MSA. Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`, use: |
|
134 | +**Standard prediction example :** |
|
135 | + |
|
136 | +``` |
|
137 | +/programs/x86_64-linux/alphafold/2.1.2/bin.capsules/run_alphafold.py \ |
|
138 | + --data_dir=/programs/local/alphafold/ \ |
|
139 | + --output_dir=/zpool_haumea/data/key/alphafold/test1 \ |
|
140 | + --fasta_paths=200.fasta \ |
|
141 | + --max_template_date=2020-05-14 \ |
|
142 | + --db_preset=full_dbs \ |
|
143 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
144 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
145 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
146 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
147 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
148 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
149 | + --model_preset=multimer \ |
|
150 | + --use_gpu_relax=True \ |
|
151 | + --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
152 | + --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta |
|
153 | +``` |
|
154 | + |
|
155 | +where test_monomer.fasta is |
|
156 | + |
|
157 | +``` |
|
158 | +>T1083 |
|
159 | +GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
|
160 | +``` |
|
161 | + |
|
162 | +**Multimer example :** |
|
163 | +``` |
|
164 | +/programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
|
165 | + --data_dir=/programs/local/alphafold \ |
|
166 | + --output_dir=$(pwd) \ |
|
167 | + --fasta_paths=${input} \ |
|
168 | + --max_template_date=2020-05-14 \ |
|
169 | + --db_preset=full_dbs \ |
|
170 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
171 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
172 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
173 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
174 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
175 | + --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
|
176 | + --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
177 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat \ |
|
178 | + --use_gpu_relax=True \ |
|
179 | + --model_preset=multimer |
|
180 | +``` |
|
181 | + |
|
182 | +where test_multimer.fasta is |
|
183 | + |
|
184 | +``` |
|
185 | +>T1083 |
|
186 | +GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
|
187 | +>T1084 |
|
188 | +MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |
|
189 | +``` |
|
190 | + |
|
191 | +### Examples - Alphafold2 2.1.1 |
|
130 | 192 | **Standard prediction example :** |
131 | 193 | ``` |
132 | 194 | /programs/x86_64-linux/alphafold/2.1.1/bin.capsules/run_alphafold.py \ |
133 | ---data_dir=/programs/local/alphafold/ \ |
|
134 | ---output_dir=/scratch/data/sbgrid/alphafold/test_monomer \ |
|
135 | ---fasta_paths=test_monomer.fasta \ |
|
136 | ---max_template_date=2020-05-14 \ |
|
137 | ---db_preset=full_dbs \ |
|
138 | ---bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
139 | ---uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
140 | ---uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
141 | ---mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
142 | ---template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
143 | ---pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 \ |
|
144 | ---obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat |
|
195 | + --data_dir=/programs/local/alphafold/ \ |
|
196 | + --output_dir=/scratch/data/sbgrid/alphafold/test_monomer \ |
|
197 | + --fasta_paths=test_monomer.fasta \ |
|
198 | + --max_template_date=2020-05-14 \ |
|
199 | + --db_preset=full_dbs \ |
|
200 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
201 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
202 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
203 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
204 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
205 | + --pdb70_database_path=/programs/local/alphafold/pdb70/pdb70 \ |
|
206 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat |
|
145 | 207 | ``` |
146 | 208 | |
147 | 209 | where test_monomer.fasta is |
... | ... | @@ -154,19 +216,20 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA |
154 | 216 | **Multimer example :** |
155 | 217 | ``` |
156 | 218 | /programs/x86_64-linux/alphafold/2.1.1/bin.capsules/run_alphafold.py \ |
157 | ---data_dir=/programs/local/alphafold \ |
|
158 | ---output_dir=/scratch/data/sbgrid/alphafold/test_multimer \ |
|
159 | ---fasta_paths=test_multimer.fasta \ |
|
160 | ---max_template_date=2020-05-14 \ |
|
161 | ---db_preset=full_dbs \ |
|
162 | ---bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
163 | ---uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
164 | ---uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
165 | ---mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
166 | ---template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files --model_preset=multimer \ |
|
167 | ---uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
|
168 | ---pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
169 | ---obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat |
|
219 | + --data_dir=/programs/local/alphafold \ |
|
220 | + --output_dir=/scratch/data/sbgrid/alphafold/test_multimer \ |
|
221 | + --fasta_paths=test_multimer.fasta \ |
|
222 | + --max_template_date=2020-05-14 \ |
|
223 | + --db_preset=full_dbs \ |
|
224 | + --bfd_database_path=/programs/local/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \ |
|
225 | + --uniclust30_database_path=/programs/local/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \ |
|
226 | + --uniref90_database_path=/programs/local/alphafold/uniref90/uniref90.fasta \ |
|
227 | + --mgnify_database_path=/programs/local/alphafold/mgnify/mgy_clusters_2018_12.fa \ |
|
228 | + --template_mmcif_dir=/programs/local/alphafold/pdb_mmcif/mmcif_files \ |
|
229 | + --model_preset=multimer \ |
|
230 | + --uniprot_database_path=/programs/local/alphafold/uniprot/uniprot.fasta \ |
|
231 | + --pdb_seqres_database_path=/programs/local/alphafold/pdb_seqres/pdb_seqres.txt \ |
|
232 | + --obsolete_pdbs_path=/programs/local/alphafold/pdb_mmcif/obsolete.dat |
|
170 | 233 | ``` |
171 | 234 | |
172 | 235 | where test_multimer.fasta is |