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Unpredictible amino acid replacements

Submitted by Victor on Wed, 2012-05-09 09:21

During loop modeling using loop_modeling.py from http://www.pyrosetta.org/scripts
and using my frag3 file for my protein I found that unpredictable amino acid replacements occur for my protein.
Could you please tell me why it is happened and how to avoid this situation,
as I do not want to change my amino acids during loop modeling.

Thank you,

Victor

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PyRosetta - General

Problems with boost

Submitted by vasek on Mon, 2012-05-07 01:56

Short story:

I get a segmentation fault when I issue:

from rosetta import *

in function PyInt_FromLong. But I am not sure what is wrong, since PyRosetta compilation worked fine.

Long story:

The binary distribution PyRosetta.MacOSX.SnowLeopard-r48781.64Bit works on my computer with the system python 2.6.1, but I would like to compile a version for the EPDPython 2.7, which I normally use. Also, I thought of this as training for a compilation on an older Centos system, for which there is no binary distribution.

I have:
-Mac OS X 10.6.8 32bit

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PyRosetta - Build/Install

symmetric docking application rosetta3.2: the docking_local_refine flag

Submitted by doranhen on Sun, 2012-05-06 02:20

Hi,
I have 2 questions regarding the high resolution stage of the symmetric docking application in rosetta3.2:
1. What exactly are the changes performed to the structure by the docking_local_refine flag (The reason I am asking this is that I want to know which clustering radius to use on the outputs and since I don't use the perturb_rigid_body_dofs flag in this stage I don't know how to set the radius for this clustering)?

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Rosetta 3 - General

Scoring with CCP4 electron density maps constraints

Submitted by xfliu on Thu, 2012-05-03 03:30

Dear all,

I have electron densities of the interface residues in CCP4 files and I want to evaluate my docking/designed models against them. It seems that Rosetta can take the "density scores" as an individual term and add it to the total Rosetta score. I am wondering if it is possible to access these functions from PyRosetta, like those living in core.scoring.electron_density. And moreover, how to calculate the pairwise scores between specific interface residues and corresponding electron densities? Any suggestions about how it works in Rosetta are also appreciated.

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PyRosetta - General

total energy score of the pdb structure

Submitted by Lindsay on Tue, 2012-05-01 12:14

Dear ALL,
I run the score_jd2 program to calculate the total energy of the pdb structure.
score_jd2.linuxgccrelease -database rosetta_database/ -s 1xnz.1.A.2.A_0001.pdb
and get a file named score.sc
SCORE: -249.622 -1098.702 251.556 555.107 2.612 11.728 -24.622 -55.572 -81.320 -24.066 -15.083 0.000 0.000 0.000 0.000 -4.476 3.227 294.517 -24.189 -40.340 0.000 0.000 0.000 1xnz.1.A.2.A_0001_0001

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Rosetta 3 - General

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