You are here


The problem hasn't been solved

Reading and writing structures using streams

Is there any way to read (write) structures (pdbs) using a python stream?
Couldn't find any clue in PyRosetta's documentation, so I guess its not a standard feature.. but I'm wondering whether there's a hack people use to in order to enable it..


Lior Z.

Post Situation: 


Good Afternoon,

We were wondering if Rosetta3.3 had the ability to use scoring as described in

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation by Will Sheffler and David Baker

We have searched the forum for how to utilize it but were not able to find a solution.

Any help would be greatly appreciated.


Post Situation: 

creating a pose from a pdb style string


is there any possibility to create a pose from a pdb style string in pyrosetta?

from the "" script I can see that pymol can be made to listen for a pdb string sent from pyrosetta. i would like to go in the other direction directly passing a pdb string to pyrosetta in order to generate a pose. is this possible? and if so what is the necessary code for this?

i know that one can generate a pose from a pdb file but i would like to skip this step in order to save the time it costs to read/write from/to disk.

Post Situation: 

Difference between score and silent_score when silent files are combined

Dear all,

I am using rosetta3.2 membrane_abinitio2 function to predict some membrane protein with 4 TM helices.
I split the prediction into 10 independent runs and each run resulted in 2000 decoys in a silent file.
When I combined these 10 silent files together, I find that the "score" changes.
Here is the score profile before combination:
SCORE: score vdw Mpair rama Menv Mcbeta Menv_non_helix Menv_termini Menv_tm_proj Mlipo hs_pair ss_pair rsigma sheet co clashes_total clashes_bb time description

Post Situation: 

RMS in Score Application

Hi all,

I am using the score.linuxgccrelease application to score my silent file (containing 20,000 structures). I am also using the -native flag to calculate an RMS for each of these structures. (I'm trying to get an RMS vs Score plot).

I am using the command:
score_jd2.linuxgccrelease -in:file:silent P001.silent.all -out:file:silent P001.silent.all.scored -out:file:silent_struct_type binary -in:file:fullatom -database $ROSETTA_DATABASE -out:file:scorefile P001.score -native ../../master/template_master.pdb

Post Situation: 

I can't find the workflow about modeling disordered regsion using rosetta?

I'm a new user of rosetta3.3
I have road the RosettaCon 2010 paper about modeling disordered regsion,
and I want to reproduce the first method result,
but I can't find the workflow of this paper.
I have got a decoy set using abinitio apps,I need the code of prediction of Disordered Segments at Termini.

Thanks a lot for your help!

Post Situation: 

Problem with sending individual energy terms using PyMOL Mover

Hi All,
I'm having a problem sending individual energy terms to PyMOL. I'm using 2.011, and going directly from the tutorial:

py = PyMOL_Mover()
py.send_energy(p, "fa_sol")

This is the error that I get:
PyMolMover.send_energy(PyMOL_Mover, Pose, str)
did not match C++ signature:
send_energy(protocols::moves::PyMolMover {lvalue}, core::pose::Pose , core::scoring::ScoreType stype=rosetta.core.scoring.__scoring_all_at_once_.ScoreType.end_of_score_type_enumeration)

Post Situation: 

Loop Modeling with fixed backbone


I wanted to model two tight turns in my protein keeping the backbone of the protein fixed. This was done to evaluate the change in the energy due to changes in loop sequence and also to look for low energy conformations. I wanted only some selected residues at those loop positions for which I made a resfile.

Here are the parameter for loop modeling :-

-loops:refine refine_kic
-loops:input_pdb 1gfl.pdb
-loops:loop_file loop_file.loop
-in:file:native 1gfl.pdb
-resfile : resfile

Post Situation: 

How does one prevent Rosetta from connecting two separate chains?

I have a homodimer of two separate chains, each one 31 residues long. I am attempting to run a comparative modeling protocol. Every pdb output has the two chains connected, which screws up subsequent relaxation.

How do I change the input fasta file, align file, and/or flags file to indicate that there are two separate chains?


Current files:
fasta file:
> Tm7_37

Post Situation: 


Subscribe to RSS - Unsolved