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set_torsion_angle error

Submitted by yijietseng on Tue, 2019-07-09 12:43
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)

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PyRosetta - General

kcenters_clustering_of_fragments

Submitted by bjharris on Mon, 2019-07-01 16:16
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

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Rosetta 3 - Applications

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

Submitted by Corvin on Wed, 2019-06-19 08:40
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.

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Rosetta 3 - Applications

Residue is not compatible with cutpoints

Submitted by iGemBoulder on Thu, 2019-06-06 08:57
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....

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PyRosetta - General

individual residue score

Submitted by yijietseng on Wed, 2019-05-29 09:59
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#)

 

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PyRosetta - General

Sampling a wider range of RMSD of poses by Rosetta Dock

Submitted by johnnytam100 on Tue, 2019-05-21 22:28
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).

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Rosetta 3 - Applications

Relax with constraints

Submitted by yijietseng on Tue, 2019-05-07 11:16
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)

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PyRosetta - General

Installation files not found

Submitted by kwadwo00 on Mon, 2019-04-29 02:51
Category: 
PyRosetta

I'm currently installing PyRosetta on windows (anaconda) using the linux tar file with the installation instructions from

http://www.pyrosetta.org/dow

I've reached step 6:

From within the new PyRosetta directory, type cd setup && python setup.py install into the command line to set up the PyRosetta.

I've run the installation and received the following output:

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PyRosetta - Build/Install

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