How to predict structures with AlphaFold: Difference between revisions
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4. Enter a jobname in the slot below the sequence slot. The results.zip filename will begin with this jobname (but none of its contents include the jobname). | 4. Enter a jobname in the slot below the sequence slot. The results.zip filename will begin with this jobname (but none of its contents include the jobname). | ||
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5. Scroll down to ''run alphafold'', ''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. | |||
* '''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. | |||
* ''tol'' (tolerance): Set this to 0.5 (or 1.0 to get a faster result). When a prediction differs from the previous "recycle" prediction by less than this value (RMSD of alpha carbons), the recycles will stop. | |||
* | |||
==References and Notes== | ==References and Notes== | ||
<references /> | <references /> | ||
