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integrativemodeling / mediator

Modeling of the yeast Mediator complex
https://salilab.org/mediator/
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How many clusters were used in the final modeling? #1

Closed benmwebb closed 8 years ago

benmwebb commented 8 years ago

Looking at the scripts in analysis/clustering/, some assume a single cluster, some 4 clusters, some 8 clusters, and some 10. And you have output models for both a single cluster and 4 clusters (although precision, density localization, and RMSF info only for the 4-cluster case). Which corresponds to the models in the actual publication?

benmwebb commented 8 years ago

The paper suggests 4. So what is the purpose of the analysis/clustering/kmeans_weight_500_1 directory?

mtrnka commented 8 years ago

In the paper, Figure 2-supplement 4 has some analysis done on "All Clusters"... this is the 1-cluster case and the directory you ask about. Everything else in the paper is on the 4-cluster analysis.

I'm not sure as to why some of the precision scripts have 10 clusters specified. It seems to be a holdover from a previous analysis that wasn't used in the paper. I don't seem to have access to our original data repository that had the analysis scripts on it.

benmwebb commented 8 years ago

Ah, I missed that figure. Thanks! All clear now.