Hi Roberto, When the AlphaFold prediction completes it loads the best model into ChimeraX. So I suggest checking periodically if any model has been loaded, for example, if len(session.models) > 0: break # AlphaFold model has been opened. Another method is to ask ChimeraX to call a callback when a model gets opened, but that would not let you detect the case where AlphaFold fails and a model is never opened. Currently Colab does not tell ChimeraX if an error occurs in sequence alignment or energy minimization -- it only appears in the AlphaFold Run html panel. Errors in the prediction phase are caught and sent to ChimeraX. I should improve this so all errors get sent back to ChimeraX. It is not obvious how to ask Colab if the jobs is still running -- Colab is meant to be run interactively through a web browser so Colab APIs are not documented to programmatically talk to it as far as I know. Tom
On Feb 15, 2022, at 5:14 AM, Roberto Marabini via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to write a script that executes "alphafold predict SEQUENCE" and then postprocess the results.
The script would be similar to:
from chimerax.core.commands import run run(session, "alphafold predict %s" % sequence_data) # wait until alphafold is done # and postprocess the file best_model.pdb
but I do not know how to implement the part "wait until alphafold is done" if, after launching alphafold, I create a loop similar to:
=== counter = 0 current_size = _getSize(file_path)
while current_size !=_getSize(file_path) or _getSize(file_path)==0 or not os.path.exists(file_path): current_size =_getSize(file_path) time.sleep(60) counter += 1 if counter > 240: # break after four hours if file is not created break ====
the loop is executed as soon as the alphafold command has been sent to google, the alphafold-colab window is not shown until the loop is finished and therefore, alphafold execution never starts.
So the question is: how can I write a script that waits until the command "alphafold predict ..." finishes and then executes some code.
Thanks
Roberto _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users