How to predict structures with AlphaFold: Difference between revisions
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* '''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. | * '''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 | * '''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 times num_models. This will proportionally increase the time to complete a result. | ||
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6. Open the Runtime menu at the very top of the page, and select '''Run all'''. | 6. Open the Runtime menu at the very top of the page, and select '''Run all'''. | ||
