The problem has been solved
Dear Rosetta users!
I am trying to build and use rosetta latest version but getting error while compiling source code with ./scons.py.
the error file is attached herewith, kinldy try to help me out.
many thanks in advance!
malkeet
Dear PyRosetta People,
I am trying to find the total score of an individual residue. This is my script so far:
scorefxn = get_fa_scorefxn()
scorefxn(pose)
AA_Score = pose.energies().residue_total_energies(5)
print(AA_Score)
It seems i get a massive print out, and when repeated for different residues gives the exact same values, so i am sure my script is wrong.
What is the correct way to get the total score for just 1 amino acid?
Hello People,
I am trying to find a way to cut out part of a protein and save to a new .pdb file.
So i have a protein and i want to cut out a section (from amino acid 315 to 330 for example), and save that cut out (and maintain the original 3D structure) into a new .pdb file.
I tried searching if there is a built-in PyRosetta function/method that does this, or if there is a script that does this, but i could not find.
Anyone can help me or guide me?
I would like to compute the whole energy of a pose object by accumulating the individual energy terms.
I have a POSE object, and a scoring fucnction called SCOREFXN. What i do is the following:
I just started working with PyRosetta, and i stumbled upon a lot of questions.
I would like to introduce rotamers, and calculate their pairwise energies, and the total energy of the system with given rotamers.
To test, i created a very simple PDB that consist only 2 amino acid.
I have the following code:
Hi Rosetta community,
I'm running the prepack protocol using as input a PDB file containing a dimer (chain A and B). The protocol seemed to work ("... reported success in 3 seconds") but I get the following warning :
[ WARNING ] When switching to a fa_standard ResidueTypeSet: Pose already contains fa_standard ResidueTypes.
and my score_sc file contains 0.000 for the total score for every generated structure.
Here the command I used to run prepack:
My pose has DNA strands and I am trying to constrain the blunt ends.
Each DNA chain is numbered starting from 1. Why can't Rosetta find the atoms?
Here is my constraint:
AtomPair C1* 1C C1* 35D HARMONIC 12.028 1.00
And here is the error:
[ERROR] Exception caught by JobDistributor for job VGK8_v2_0001Atom 'C1* 1359' not found
Dear Rosetta Users,
I am having a problem with the antibody_prepack_protocol, I am again following the Nature Protocols article “Modeling and docking of antibody structures with Rosetta” (doi:10.1038/nprot.2016.180).
Short Story:
I get the following error when I run the prepacking protocol on my antibody, but only when I switch the heavy and light chains from HL to LH:
ERROR: (end_res_ - start_res_ + 1) == conf_size_
Long Story:
Hi,
Im trying to cmpile Rosetta 3.7 with openmpi and getting the following errors. Please help.
Environmet: Centos 7.3
Modules loaded : GCC/6.1.0, openmpi/1.10.2
mpicc --version
gcc (GCC) 6.1.0
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