how to calculate RMSD using hickit

zhang-jiankun commented 5 years ago

Hello @lh3 @tanlongzhi In the Dipc code written by Tan, Align.py can calculate the root mean square deviation of the three-dimensional structure of each round of modeling at a given final resolution. Does hickit have a similar function? Or how do we determine the final resolution we can get is reliable when using hickit? Thanks for the help!

tanlongzhi commented 5 years ago

On the dip-c side, I recent wrote some format-conversion scripts, so you can always convert hickit contacts and 3D structures for analysis in dip-c:

scripts/hickit_impute_pairs_to_con.sh impute.pairs.gz
for rep in `seq 1 3`
do
  scripts/hickit_3dg_to_3dg_rescale_unit.sh 20k.${rep}.3dg
  dip-c clean3 -c impute.con.gz 20k.${rep}.dip-c.3dg > 20k.${rep}.clean.3dg
done
dip-c align -o aligned.20k. 20k.[1-3].clean.3dg 2> 20k.align.log > 20k.align.color

I'll update dip-c's manual page when our next paper comes out in the upcoming months.

zhang-jiankun commented 5 years ago

Thanks!

lh3 / hickit

how to calculate RMSD using hickit #18