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hiclib / pastis

Poisson-based algorithm for stable inference of DNA Structure
http://hiclib.github.io/pastis/
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Annotation of pdb #18

Open robinweide opened 8 years ago

robinweide commented 8 years ago

Hi all,

Firstly for the devs: awesome work! Very impressed by both the code and docs.

I have made some nice looking structures (PM1@150000bp bins), which I would love to annotate -using BED-files- with AB-status, genes etc.

Since I'm very new with this and especially the pdb format, I need some help with this. Could you give me some hints how to assign a color (or element-type) to individual atoms of the pdb?

Thank you, Robin

NelleV commented 7 years ago

Hi robinweide,

Sorry for the very late reply. I seem to have problems with github emails.

Unfortunately, there is no easy way of doing this. I think you will have to build your own scripts to do the visualization, and map which portions of the genomes corresponds to your bed file. I usually use mayavi for visualization, which allows to provide a color for each element plotted, but finding the mapping between beads and colors is the tricky part.

Thanks, N