You are here

Home

Unsolved

The problem hasn't been solved

Making mutations in PyRosetta?

Submitted by thorx020 on Thu, 2012-08-09 09:24

Hi all,

I'm new to PyRosetta and just had a quick question. Is there a way to make mutations to an existing protein structure using PyRosetta? I'm currently doing all the mutations in PyMOL then saving the mutants as new pdb's and calling them into PyRosetta for analysis. If I could just write a short script to mutate the structure using PyRosetta, it would save me a lot of time. Thanks!

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

ndruns and nstruct in fixbb

Submitted by Anonymous on Tue, 2012-08-07 01:52

In manual for fixbb in Rosetta 2.x, ndruns is used to specify the number of iterations. In the manual for fixbb in Rosetta 3.x, the parameter ndruns is not introduced anymore. Rather, nstruct is used to specify "The number of iterations to perform per input structure". Does it mean nstruct has replaced ndruns? Or is ndruns the same as nstruct but only one decoy (the best scoring decoy) is returned?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

RNA Denovo RMSD data

Submitted by eremma on Thu, 2012-08-02 01:40

Hi,
I am new to the Rosetta software and I would really appreciate some help from someone with experience in RNA Denovo. I am using the rna_denovo application on a cluster with Rosetta 3.3 and I want to predict 3D structures for a large number of RNA molecules.
Initially I predict 3D structures for which there is NMR data available so that I can determine how well the algorithm works. I am supplying the NMR structure as the native structure in order to plot RMSD vs. energy (score).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Scoring when the protein is a different length

Submitted by gw on Wed, 2012-08-01 08:53

I would like to truncate a protein (the C terminus). I'm not sure where - the segment is about 70 residues long and is 3 helices with short loop segments of a few residues connecting them. Rather than make 70 truncation mutants in the lab I thought I could narrow it down by comparing the scores of truncated PDBs.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

how to output a structure when scoring it?

Submitted by tianbu on Tue, 2012-07-31 09:38

Dear all,
I use score_jd2 to score a pdb structure. But I also want to output the structure.
I try ~/software/Rosetta_3.4/rosetta_source/bin/score_jd2.linuxgccrelease -s 1f0m.pdb -database ~/software/Rosetta_3.4/rosetta_database -out:prefix 1f0m_test -out:output
But I didn't get the structure. I only get the 1f0m_test.sc which contains the energy of the pdb.

I think I have found the reason. I should use score instead of using score_jd2
But the structure output by score has more H atom than original one. Is that will change the energy score? Thank you!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

ab initio membrane error (frag9 file...)

Submitted by almeida on Mon, 2012-07-30 08:53

Hi all...

I'm running the ab initio membrane app as...

almeida@IDBiotum7:/modelacion/Rosetta$ membrane_abinitio2.linuxgccrelease -abinitio:membrane -in:file:fasta ../P13866.fasta -in:file:spanfile sglt1.span -nstruct 5 -in:path:database /home/almeida/Softwares/Rosetta/rosetta_3.4/rosetta_database/

... and I got this error: 'ERROR: Value of inactive option accessed: -in:file:frag9'

How do I generate the frag9 file for my protein sequence?

Thanks in advance...

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Error Atom_::dihedral_between_bonded_children

Submitted by abiadak on Mon, 2012-07-30 06:34

Hi, I'm running the example homology_modeling_threading_basic from the demos with minirosetta ver. 3.4 and fails whith

ERROR: Atom_::dihedral_between_bonded_children: atoms are not both my children!
ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 407

when setting the flag:

-out:nstruct 10

If compiled with gcc 4.4 (x86_64) it happens while generating fifth model and when compiled with icc 12.1 (x86_64) it happens while generating third model.

Any help would be welcome.

Thanks!

David.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How to insert a TER line between docking partners

Submitted by devroop on Sun, 2012-07-29 13:48

Can anyone please help regarding how to insert a TER line between docking partners (in the pdb of the docked complex)? Actually, I have the pdb file of a docked protein-protein complex(generated by a global docking platform). Now I need to prepare the input file (pdb) for a local docking search using Rosetta. So I need to insert a TER line between the docking partners.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages