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hello,

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

from the "PyMOLPyrosettaServer.py" 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.

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

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.apply(p)
score(p)
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)

Hi,

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:fullatom
-in:file:native 1gfl.pdb
-resfile : resfile
-ex1
-ex2
-loop:fix_natsc
-loop:refine_repack_cycles