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Resfile Error

Category: 
PyRosetta

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:

Post Situation: 

set_torsion_angle error

Category: 
Small Molecules

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)

Post Situation: 

Pyrosetta: restrict repack (and minimization) to specific region

Category: 
PyRosetta

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:

Post Situation: 

kcenters_clustering_of_fragments

Category: 
Fragment Generation

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

Post Situation: 

Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking

Category: 
Loop Modeling

Dear Sir or Madam,

I got a one complicated problem, which took place during loop modelling for protein-protein docking. I carry out tasks from the Meiler tutorial for Rosetta.

Post Situation: 

Residue is not compatible with cutpoints

Category: 
PyRosetta

Hi all,

I'm currently trying to run the CCDLoopClosureMover function in order to attach two protein domains together. 

When I try to add a single cutpoint variant around my jump point, I repeatedly get a warning that says:

"Residue 126 is not compatible with cutpoints; variant type not changed." 

Residue 126 is the Cterminus

This warning also shows up for residue 127 (the Nterminus of the other protein domain). And thus, I cannot apply CCD to my pose because I don't have a cutpoint variant....

Post Situation: 

individual residue score

Category: 
Scoring

Hi all,

I just have a question about the individual AA score. So I am trying to compare the total score (with proper weighted scoreterms) and the individual AA score. 

For the total score I used:

scorefxn = get_fa_scorefxn()

score = scorefxn(pose)

To get the weighted indicidual AA score I used:

pose.energies().residue_total_energy(residue#)

 

Post Situation: 

Sampling a wider range of RMSD of poses by Rosetta Dock

Category: 
Docking

Hi, I am designing a protein interface of a nanobody with my target antigen.

1000 initial poses were generated by patchdock and 1000 designs were generated per each pose.

After ploting the ddg-rmsd scatter plot, I found all the poses has a characteristic scatter plot like fig. A attached (a narrow RMSD range within ~0.25A, while a majority stays exactly at 0.00A).

Post Situation: 

Relax with constraints

Category: 
Constraints

Hi everyone,

I am a newbee in Pyrosetta, and I am trying to learn how to relax with constraints. I wanted to do distance constraints, but I am not sure if I am doing it right or wrong at all.  The score came out to be almost the same for with and without the constraint. Can anyone give me any advise? 

#------------------------Set up Score Function-----------------------

scorefxn = get_fa_scorefxn() 
score_before = scorefxn(pose)

Post Situation: 

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