Oliver Clarke

Ok thank you Ruben will do! The reason I asked is because we have had trouble with these cards not working with other programs that rely on earlier versions of...

Hi Paul, no I mean on this plot: When I click on a residue, it recenters on a residue. What I am suggesting is to (a) highlight the currently centered...

Yes, this is an option - I have done it this way in the past.

No alignment means smaller chance of overfitting, but we often use higher T-values with skip-align classifications in order to resolve subtle differences - in this case maybe there is some...

Will do - running jobs right now with/without blush to test.

@biochem-fan @dkimanius I can't say yet whether it is going to be useful downstream, still running tests, but what I will say is that the resulting classification volumes are a...

Yes, the results are very different in terms of class distribution in matched runs, so it is clearly making a difference - for some cases that could be good, in...

Just noting here that there is now at least one example where BLUSH plus no-align classification has proven useful: https://x.com/BJ_Greber/status/1758778828292247617?s=20 https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae107/7609228?login=false

This is very handy advice, thanks Ellen! I wonder if a non-default mask is supplied, maybe the mask name should be added to the subdirectory name in the same way...

Thanks Ellen - sorry I overlooked that there was already one for preprocess, you're right it does exist!