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Clustering problem

Category: 
Scoring

Hi guys.

I met a problem when I was doing the clustering. I excuted this command but it was unexpectedly ended killed and had no result. I've 200 pdb files in this folder.

I'll be really grateful if it can be solved.

$ /home/suuo/Rosetta/main/source/bin/cluster.default.linuxgccrelease -database /home/suuo/Rosetta/main/database -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out in:file:s *.pdb

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Post Situation: 

PDB Clustering

Category: 
Scoring

Hello,

I was working on homology modeling and built 1000 models with ligands. I'm planning to select 100 top scored models and do clustering on them.

I tried cluster.linuxgccrelease, but the program didn't recognize the ligand. I specified the option -exclude_res, but it didn't work. 

I also tried calibur.linuxgccrelease, but there are a lot of warnings instead of the output.

I'm attaching the log files. Can you help me with these issues? Thank you in advance!

 

Post Situation: 

Show I be using beta_nov16 scorefxn?

Category: 
Scoring

ref2015 is the default at least in pyrosetta and is beta_july15 without the need for the boolean option `correction:beta_july15` to be set.

In the cartesian ddG paper, Park et al. 2016, beta_nov16 is made, which has several difference (below, code used here).

Post Situation: 

Atom-wise energy terms from nearest N-neighbors

Category: 
Scoring

Hello PyRosetta users,

Can you please advise me on how I should go about calculating atom-wise energy terms?

Should I simply sum pairwise energies for the nearest N-neighbours or is there a better way of doing this?

 

Thanks!

Post Situation: 

Individual Residue Energy

Category: 
Scoring

Hi everyone,

I'm trying to get the energies of individual residues in a pose and am encountering an error that I can't seem to find much information on. Here is a sample of my script:

from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.rosetta.core.scoring import *

pyrosetta.init('-ignore_zero_occupancy false')

pose = pose_from_pdb(pdb_file)

sfxn = create_score_function('ref2015.wts')

score = pose.energies().residue_total_energy(1)

And here is the error I encounter:

Post Situation: 

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