840233c6a9ea4403bf2f18606e7ccf8853bb54e7
examples/alphafold2.md
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7 | 7 | - [Running the python script run_alphafold.py](#running-the-python-script-run_alphafoldpy) |
8 | 8 | - [GPU Memory](#gpu-memory) |
9 | 9 | - [Web portal](#web-portal) |
10 | - - [Changes in AlphaFold 2.1.1 multimer](#changes-in-alphafold-211-multimer) |
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11 | - - [Examples - Alphafold2 2.1.2](#examples---alphafold2-212) |
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12 | - - [Examples - Alphafold2 2.1.1](#examples---alphafold2-211) |
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10 | + - [Changes in latest versions](#changes-in-latest-versions) |
|
11 | + - [Examples](#examples) |
|
13 | 12 | - [Known issues](#known-issues) |
14 | 13 | |
15 | 14 | <!-- /TOC --> |
... | ... | @@ -109,7 +108,12 @@ XLA_PYTHON_CLIENT_ALLOCATOR=platform |
109 | 108 | It is possible to run alphafold through a web portal. See |
110 | 109 | https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb . |
111 | 110 | |
112 | -### Changes in AlphaFold 2.1.1 multimer |
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111 | +### Changes in latest versions |
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112 | +**2.1.2** |
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113 | +Version 2.1.2 adds a few new features that must be explictly defined on the command line. |
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114 | +See the examples below for and example and `run_alphafold.py --help` for more info. |
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115 | + |
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116 | +**2.1.1** |
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113 | 117 | 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. |
114 | 118 | |
115 | 119 | To use it, set the ALPHAFOLD_X variable to 2.1.0 in the shell or in the ~/.sbgrid.conf file. |
... | ... | @@ -128,10 +132,11 @@ This is the standard SBGrid version override method. |
128 | 132 | 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. |
129 | 133 | |
130 | 134 | |
131 | -### Examples - Alphafold2 2.1.2 |
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135 | +### Examples |
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132 | 136 | **NOTE : Alphafold2 introduced new flags for GPU-based relaxation that must be specifed**. |
133 | 137 | You can also resume from a previously run MSA. See [the alphafold2 github repo](https://github.com/deepmind/alphafold/releases/tag/v2.1.2) for more info. |
134 | 138 | |
139 | +**Alphafold2 2.1.2** |
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135 | 140 | **Standard prediction example :** |
136 | 141 | Assuming Alphafold2 databases and parameters are in `/programs/local/alphafold`, use: |
137 | 142 | |
... | ... | @@ -160,7 +165,7 @@ where test_monomer.fasta is |
160 | 165 | >T1083 |
161 | 166 | GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
162 | 167 | ``` |
163 | - |
|
168 | +**Alphafold2 2.1.2** |
|
164 | 169 | **Multimer example :** |
165 | 170 | ``` |
166 | 171 | /programs/x86_64-linux/alphafold/${ALPHAFOLD_X}/bin.capsules/run_alphafold.py \ |
... | ... | @@ -190,7 +195,7 @@ GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAA |
190 | 195 | MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH |
191 | 196 | ``` |
192 | 197 | |
193 | -### Examples - Alphafold2 2.1.1 |
|
198 | +**Alphafold2 2.1.1** |
|
194 | 199 | **Standard prediction example :** |
195 | 200 | ``` |
196 | 201 | /programs/x86_64-linux/alphafold/2.1.1/bin.capsules/run_alphafold.py \ |
... | ... | @@ -215,6 +220,7 @@ where test_monomer.fasta is |
215 | 220 | GAMGSEIEHIEEAIANAKTKADHERLVAHYEEEAKRLEKKSEEYQELAKVYKKITDVYPNIRSYMVLHYQNLTRRYKEAAEENRALAKLHHELAIVED |
216 | 221 | ``` |
217 | 222 | |
223 | +**Alphafold2 2.1.1** |
|
218 | 224 | **Multimer example :** |
219 | 225 | ``` |
220 | 226 | /programs/x86_64-linux/alphafold/2.1.1/bin.capsules/run_alphafold.py \ |