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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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Regarding exp.py #18

Closed tarak77 closed 5 years ago

tarak77 commented 5 years ago

Hi @tanlongzhi , In exp,py, will it possible to include an option for translating the chromosomes instead of the two homologs separately? I mean instead of finding the centers of each homolog, can we find the centers of the homolog pair and then translate.

tanlongzhi commented 5 years ago

Hi Tarak,

Unfortunately, dip-c exp currently doesn't offer this function.

However, you can easily manipulate .3dg files yourself. The format is extremely simple, whose columns 3-5 can be directly modified with any software. It's a plain-text format whose ordering of lines doesn't matter.

tarak77 commented 5 years ago

Happy thanksgiving @tanlongzhi ! I see, I was looking at pymol_movie_exp.py script for making a movie. I understand it now: extracting each chromosome as a separate object and then defining the timeframe for movie and translating and then rotating it.

I was trying to modify it so that in my movie: ->First 360deg loop shows us the whole genome ->second loop shows just the chromosome1(maternal and paternal) and hides the other chromosomes ->third loop shows just chromosome2(mat and pat) and hides others ->forth loop shows just chromosome3(mat and pat)... ...... ->last loop shows just chromosome X and Y

I was playing with the script but I couldn't get the frames setting right and get what I want. I would really appreciate if you could help me with the rough template for the task above?

Hope to hear from you soon!

tanlongzhi commented 5 years ago

Happy holidays Tarak!

I'm afraid that my knowledge about PyMol is not sufficient to answer your question. My script was put together after trials and errors, without much understanding. You can probably ask for help from structural biologists, who should be experts on PyMol.

For your purpose, I'd probably do each loop separately, and then concatenate the movies afterwards.

tarak77 commented 5 years ago

Sure, ill try out doing them separately. Thanks!

tarak77 commented 5 years ago

I somehow managed to get the movie using one script. I defined scenes for different tasks.

tanlongzhi commented 5 years ago

Happy to hear! Best wishes on moving directing!