The problem has been solved
There is a flag that I cannot recall that stops Rosetta from using ligand params from PDB and instead use the one from n:file:extra_res_fa and n:file:extra_res_cen.
What is it? I cannot find it in my notes and in the documentation.
Hello,
I wonder if naive protein structure can be predicted by using true distance and angle constraints.
If we can do that, how do we choose rosetta applications and parameters?
Hello,
I'm using antibody protocl to graft some models but it fails with the following error:
File: src/protocols/antibody/grafting/chothia_numberer.cc:152
ERROR: Unxpected length of light-fr3 [length=31], length expected to be: [32, 33, 34]!
Do you have any comments on this? I have three sequences (three different antibodies with light and heavy chains) and it works on one of them but the same error on the two others.
Thanks a lot in advance,
Best
Hi all,
I'm trying to run the molfile_to_params.py script.
I run into an import error: "No module named rosetta_py.io.mdl_molfile"
Anyone know where I can find and download rosetta_py for pyrosetta?
I can't seem to find it online...
Thank you
Hi
I'm a postgraduate student, interested in protein structure prediction.
I noticed that the document said:
So, I want to know, how to use rosetta to predict number of protein of amino acids more than 150 (e.g. 500)?
Hello everyone,
I am trying to perform RosettaDesign, and I have a script that uses pyrosetta.rosetta.core.pack.task.parse_resfile()
In the past this worked just fine, but now with the new update it seems it doesn't work, I get this error:
RuntimeError:
File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_$ main/source/src/core/pack/task/ResfileReader.cc:1582 [ ERROR ] UtilityExitException ERROR:
I am not sure how to fix this issue, following is two codes that break:
Hi all,
I created a customized ligand, and we want to sample different rotamers around certein bonds by changing the torsion angles. And below is what we have done and we ran into an issue:
atom1 = AtomID(13,1)
atom2 = AtomID(14,1)
atom3 = AtomID(15,1)
atom4 = AtomID(16,1)
old_torsion_angle = pyrosetta.rosetta.core.conformation.Conformation().torsion_angle(atom1, atom2, atom3, atom4)
print (old_torsion_angle)
Hi everyone,
I am trying to restrict repacking around a residue . I have written a script with PreventRepacking() and RestrictToRepacking but I am still confised about the result. Here is the code I am using:
Hello Rosetta community,
I'm having trouble finding the fragment generation application "kcenters_clustering_of_fragments." The application is mentioned as publically available in the methods section of D.A. Silva et al (2019). De novo design of potent and selective mimics of IL-2 and IL-15. Nature. Link: https://www.nature.com/articles/s41586-018-0830-7?WT.feed_name=subjects_computational-biology-and-bioinformatics
Hello all,
I am currently working with the crystal structure of the ARAC protein domain and need a better understanding of the built in Classic Relax function.
