How to predict structures with AlphaFold: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) |
||
| Line 22: | Line 22: | ||
5. Scroll down to the section titled ''run alphafold'', subsection ''Sampling options'': | 5. Scroll down to the section titled ''run alphafold'', subsection ''Sampling options'': | ||
* '''num_models''', the number of models to be predicted, is 5 by default. You could reduce this to 3 if you are in a hurry. | * '''num_models''', the number of models to be predicted, is 5 by default. You could reduce this to 3 if you are in a hurry. | ||
* '''max_recycles''': Set this to 48 (or at least 12). The actual number of "recycles" performed will stop when the model has converged to the specified tolerance. The default of 3 is often not enough for an optimal result. | * '''max_recycles''': Set this to 48 (or at least 12). The actual number of "recycles" performed will stop when the model has converged to the specified tolerance. The default of 3 recycles is often not enough for an optimal result. | ||
* '''tol''' (tolerance): Set this to 0.5 Å (or 1.0 to get a faster result). When a prediction differs from the previous "recycle" prediction by less than this value (RMSD in Å between alpha carbons), the recycles will stop. | * '''tol''' (tolerance): Set this to 0.5 Å (or 1.0 to get a faster result). When a prediction differs from the previous "recycle" prediction by less than this value (RMSD in Å between alpha carbons), the recycles will stop. | ||
* '''num_samples''' (random seeds): Leave this at 1. Beware that if you increase this above 1, you will generate a number of models equal to the product of this value and num_models. This will proportionally increase the time to complete a result. | * '''num_samples''' (random seeds): Leave this at 1. Beware that if you increase this above 1, you will generate a number of models equal to the product of this value and num_models. This will proportionally increase the time to complete a result. | ||
