a4074bf7bc3ae45a66978ac41adc953f7c371d1f
examples/alphafold2.md
| ... | ... | @@ -11,6 +11,7 @@ |
| 11 | 11 | - [pTM scores](#ptm-scores) |
| 12 | 12 | - [Examples](#examples) |
| 13 | 13 | - [Web portal](#web-portal) |
| 14 | + - [Changes in AlphaFold 2.1.0](#changes-in-alphafold-210) |
|
| 14 | 15 | - [Known issues](#known-issues) |
| 15 | 16 | |
| 16 | 17 | <!-- /TOC --> |
| ... | ... | @@ -143,6 +144,40 @@ run_alphafold.sh /programs/x86_64-linux/alphafold/2.0.0/alphafold/data/T1050.fas |
| 143 | 144 | It is possible to run alphafold through a web portal. See |
| 144 | 145 | https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb . |
| 145 | 146 | |
| 147 | + |
|
| 148 | +### Changes in AlphaFold 2.1.0 |
|
| 149 | +On 4 Nov 2021 we added vesion 2.1.0 to the installation. This version allows prediction of multimers from fasta files containing multiple sequences. This version is not currently the default, but will be after further testing. |
|
| 150 | + |
|
| 151 | +To use it, set the ALPHAFOLD_X variable to 2.1.0 in the shell or in the ~/.sbgrid.conf file. |
|
| 152 | +This is the standard SBGrid version override method. |
|
| 153 | + |
|
| 154 | +**NOTE** |
|
| 155 | +- Databases must be redownloaded, specifically UniProt and PDB seqres databases. |
|
| 156 | + - Run `scripts/download_uniprot.sh <DOWNLOAD_DIR>`. |
|
| 157 | + - Remove/rename `<DOWNLOAD_DIR>/pdb_mmcif`. It is needed to have PDB SeqRes and PDB from exactly the same date. Failure to do this step will result in potential errors when searching for templates when running AlphaFold-Multimer. |
|
| 158 | + - Run `scripts/download_pdb_mmcif.sh <DOWNLOAD_DIR>`. |
|
| 159 | + - Run `scripts/download_pdb_seqres.sh <DOWNLOAD_DIR>`. |
|
| 160 | +- Update the model parameters. |
|
| 161 | + - Remove/rename the old model parameters in `<DOWNLOAD_DIR>/params`. |
|
| 162 | + - Download new model parameters using `scripts/download_alphafold_params.sh <DOWNLOAD_DIR>`. |
|
| 163 | + |
|
| 164 | +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. |
|
| 165 | + |
|
| 166 | +Multimer example : |
|
| 167 | + |
|
| 168 | +``` |
|
| 169 | +/programs/x86_64-linux/alphafold/2.1.0/bin.capsules/run_alphafold.py --data_dir=/scratch/data/sbgrid/alphafold-2.1.0 --output_dir=/scratch/data/sbgrid/alphafold/test4 --fasta_paths=test4.fasta --max_template_date=2020-05-14 --db_preset=full_dbs --bfd_database_path=/scratch/data/sbgrid/alphafold-2.1.0/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path=/scratch/data/sbgrid/alphafold-2.1.0/uniclust30/uniclust30_2018_08/uniclust30_2018_08 --uniref90_database_path=/scratch/data/sbgrid/alphafold-2.1.0/uniref90/uniref90.fasta --mgnify_database_path=/scratch/data/sbgrid/alphafold-2.1.0/mgnify/mgy_clusters_2018_12.fa --template_mmcif_dir=/scratch/data/sbgrid/alphafold-2.1.0/pdb_mmcif/mmcif_files --model_preset=multimer --uniprot_database_path=/scratch/data/sbgrid/alphafold-2.1.0/uniprot/uniprot.fasta --pdb_seqres_database_path=/scratch/data/sbgrid/alphafold-2.1.0/pdb_seqres/pdb_seqres.txt --obsolete_pdbs_path=/scratch/data/sbgrid/alphafold-2.1.0/pdb_mmcif/obsolete.dat |
|
| 170 | +``` |
|
| 171 | + |
|
| 172 | +where test4.fasta is |
|
| 173 | + |
|
| 174 | +``` |
|
| 175 | +>T1083 |
|
| 176 | +GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
|
| 177 | +>T1084 |
|
| 178 | +MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |
|
| 179 | +``` |
|
| 180 | + |
|
| 146 | 181 | ### Known issues |
| 147 | 182 | - Some newer GPUs that require CUDA 11.1 or later may not be able to run this version of Alphafold. An update is planned that should correct this. |
| 148 | 183 | - Unified memory across GPUs does not appear to work in the current version. |