You are here

Coding denovo prediction from density maps in PyRosetta

2 posts / 0 new
Last post
Coding denovo prediction from density maps in PyRosetta
#1

I want to code the below scripts using PyRosetta. I'm totally new to Pyrosetta, only starting to read the tutorials today. However, I know Python very well. Anyway, all the scripts seem to be calling the denovo_density.linuxgccrelease binary so I'm guessing, if there's a Pyrosetta class or module built on that, it shouldn't be but a few lines of code.

My qustions are, can it be done? How? 

 

#!/bin/sh


mkdir round3_alpha_tubulin

$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
	-in::file::fasta /home/labusr/Documents/tubulin_exercise/5ucy_alpha.fasta\
	-fragfile /home/labusr/Documents/tubulin_exercise/9mers_alpha\
	-startmodel /home/labusr/Documents/round2_alpha_tubulin.pdb \
	-mapfile /home/labusr/Documents/tubulin_exercise/masked_map_center_alpha.mrc\
	-n_to_search 1000 -n_filtered 4500 -n_output 50 \
	-bw 16 \
	-atom_mask_min 2 \
	-atom_mask 3 \
	-clust_radius 3 \
	-clust_oversample 4 \
	-point_radius 3 \
	-movestep 1 \
	-delR 2 \
	-frag_dens 0.8 \
	-ncyc 3 \
	-min_bb false \
	-pos $1 \
	-out:file:silent round3_alpha_tubulin/alpha_tubulin.$1.silent

 

#!/bin/sh

$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
	-mode score \
	-in::file::silent round3_alpha_tubulin/alpha_tubulin*silent \
	-scorefile round3_alpha_tubulin/scores3 \
	-n_matches 50

 

#!/bin/sh

$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
	-mode assemble \
	-nstruct 5 \
	-in::file::silent round3_alpha_tubulin/alpha_tubulin*silent \
	-scorefile round3_alpha_tubulin/scores3 \
	-assembly_weights 4 20 6 \
	-null_weight -150 \
	-out:file:silent round3_alpha_tubulin/assembled.$1 \
	-scale_cycles 1 \
	-mute core

 

#!/bin/sh

$ROSETTA3/source/bin/denovo_density.linuxgccrelease\
	-mode consensus \
	-in::file::silent round3_alpha_tubulin/assembled.*silent \
	-consensus_frac 0.8 -energy_cut 0.05 \
	-mute core

# use the old model as a starting point
cp S_0001.pdb round3_alpha_tubulin.pdb

 

Category: 
Post Situation: 
Tue, 2018-04-10 11:43
ahmadkhalifa

Unfortunately, much of the functionality of the denovo_density application is in the application file itself, and so is not included with PyRosetta. -- The code is also very commandline centric, with input/output reading/writing interspersed with the calculation code.

If you take a look at $ROSETTA3/source/src/apps/public/electron_density/denovo_density.cc, you can see how things are implemented. If you can interpret C++ well enough, you may be able to ascertain how the application does what it does, pull out the parts you're interested and come up with a PyRosetta-equivalent protocol. It'll be more than a few lines of code, though.

 

Tue, 2018-04-10 15:29
rmoretti