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