# Coding denovo prediction from density maps in PyRosetta

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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