change resolution from .3dg file

tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data

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change resolution from .3dg file #35

Closed lidaof closed 5 years ago

lidaof commented 5 years ago

Hi Tan @tanlongzhi , I downloaded some .3dg file from your GEO repository, i found most of them are based on 20kb resolution. Is it possible I can convert them to 40kb, 80kb without remodeling? i was thinking if convert to 40kb for example, we can use the center point of 2 points (atoms) from 20kb file? does this make sense?

tanlongzhi commented 5 years ago

Hi @lidaof, you're right that we only kept the 20-kb files for all cells. I think the results will be different between a normal 40-kb run and a back-calculated one; you can try a few cells and compare. I suspect problems especially with length scaling.

As a side note, 3D modeling to 40 kb (or 80 kb) is very fast with the current hickit pipeline, and is much faster than running to full 20 kb. So it won't take long if you re-run.

lidaof commented 5 years ago

Hi @tanlongzhi thanks for reply. seems back calculation may not a good choice. Do you know which tool can compare 2 3d models? Thanks again

tanlongzhi commented 5 years ago

No problem. You can use dip-c align to align (via rotation, translation, and/or mirror image) multiple 3D models. This should make visual comparison easier in PyMol.

lidaof commented 5 years ago

Thank you @tanlongzhi !