The problem hasn't been solved
I'm trying to run a ReportFSC mover between two maps to debug some issue in my structure refinement protocol (https://www.rosettacommons.org/node/10195). I'm fairly new to Rosetta scripting, below you can find my attempt. What am I doing wrong? Thanks in advance.
Good morning,
I have a database of dihedral angles in this order: residue psi psi. Is is possible to use pyrosetta to sample randomly throuh this database,
applying random psi and psi angles to a pdb pose, using a movemap? Imagine that my sequence is AQAAVFGT; so the script would retrieve randomly from the database the dihedrals corresponding to residues in the sequence and output a pose.
is this possible? Maybe with a loop with the SetTorsion mover?
Thank you,
cheers
I am working on ligand-based protein design by rosetta. I am getting a constant error on the rosetta matching algorithm to find possible binding sites in the protein molecule for the desired ligand. The error that I receive is "Cannot normalize xyzVector of length() zero". I tried running the script on different servers and multiple times but I get the same error everytime. What could possibly be going wrong?
I am trying to run the ddg_monomer high-res protocol on a protein. I am running this on a Linux system with 4 GB of RAM. Immediately after the protocol begins to run, RAM usage gets very high and my computer freezes. It remains frozen indefinetely. Is this normal? Usually when I run other ROSETTA protocols, the computer is perfectly usable with the job running in the background.
I am using all the default settings from the high-res protocol (row 16 of Kellogg et al) from the documentation:
Hi everyone,
We are trying to replicate the experiment by Alford et al. (2017) in our lab to calculate the ΔΔG of T193V mutation for the RT-RH-derived peptide bound to HIV-1 protease (PDB entry 1kjg). However, we have been getting values that are different from the reported ΔΔG of –4.95 kcal/mol and it’s likely due to errors in our code.
I have a few questions regarding this tutorial here:
https://www.rosettacommons.org/demos/latest/public/electron_density_structure_refinement/structure_refinement
1) What does ReportFSC do exactly? Does it generate a density map from the atomic model and correlates it to the test map?
Dear All,
I am using rosetta_bin_linux_2017.52.59948_bundle to run demos/public/ideal_proteins. The running command is
"rosetta_scripts.static.linuxgccrelease -s input.pdb -parser:protocol input.xml -nstruct 10 -restore_talaris_behavior".
Since I got
"
score_typeextract failed: fa_plane
ERROR: bad line in file myweight.wts:fa_plane 0
ERROR:: Exit from: src/core/scoring/ScoreFunction.cc line: 453
I tried to run the below script in Python to automate some stuff:
Dear all,
I am following the tutorial http://2016.rosetta.ninja/day-3/rosettaremodel-basic-tutorial.
I am using version 2017.52, and run command "nohup remodel.static.macosclangrelease -s 1pgaA_0001.pdb -blueprint template.blueprint -jd2:no_output -num_trajectory 1 -save_top 1 -out:prefix long_loop -remodel:quick_and_dirty > output.txt"
The output.txt was attached. No long_loop_1.pdb can be found.
Many thanks.
I am teaching myself rosetta scripts. I followed the tutorial https://www.rosettacommons.org/demos/latest/tutorials/scripting_with_rosettascripts/scripting_with_rosettascripts#altering-the-pose-movers_packing_repacking-sidechains
One of the interesting thing is