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- OS type,
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for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

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Thank you!

Post Situation: 

What is the expected behaviour when minimizing a jump edge?

Category: 
Docking
Constraints
PyRosetta

I have seen references to minimization of a jump edge (e.g using a MinMover object) leading to both rotations and translations downstream of the jump. 

I am modelling an interaction between two proteins, connected in the fold tree by a single jump edge, with atom pair constraints defined to bring them into close proximity.

I allow movement of this jump in the movemap (set_jump), atom_pair_constraints is activated in the scorefunction, and the fold tree is valid.  

Post Situation: 

Minimization not changing jump edge vector length

Category: 
Docking

I have written a script using PyRosetta (pyrosetta-4.0-py2.7 retrieved from github 2017-05-23) which:
- imports a PDB file containing a full antibody structure and antigen dimer separated by around 100A
- defines a custom fold tree with the Fc at the root and a jump edge connecting the Fc to the antigen
- creates ambiguous site constraints consistent with interaction of variable loops of the two Fab domains with the epitope of each antigen in the dimer

Post Situation: 

EnergyMethodCreator error when writing custom energy method

Category: 
Design

Hi,

I have been trying to write a custom energy method class  following the workshop #11 from the Gray lab and this tutorial http://graylab.jhu.edu/pyrosetta/downloads/scripts/test/T850_SubClassing.py . Here is what I have:

Post Situation: 

Rosetta compilation on Linux Ubuntu

Category: 
Compilation

Hi everyone,

I downloaded the rosetta package for linux (version 3.8). During the compilation I receive an error saying: 

UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 102: ordinal not in range(128)
scons: building terminated because of errors.

Can someone help me to resolve this problem. Thank you.

Post Situation: 

how to generate the whole molecule that contains all the symmetric chains

Category: 
Symmetry

Dear all,

I have a pdb file which contains three chains (A, B, and C) for a protein molecule. According to my knowledge, the protein should be 3-fold symetric and a trimer of the three chains. Is there a way to generate the pdb file which contains all the 9 chains for the whole molecules?  I can only find some infomation from the original pdb file about the symmetry like these:

Post Situation: 

Interesting scoring performance in flexpepdock against random peptides

Category: 
Scoring

Dear all,

recently I have tried to dock some different peptides to binding pocket of protein kinase and see their performance in flexpepdock. In the meanwhile I also dock some random peptides, such as poly G (GGGGGSGG) and poly E peptide(EEEEESEE). Interestingly, the energy score of good peptides and random peptides didn't show much differences(from -650 to -690), sometimes the random peptides even showed the better energy score. In order to keep them in the pocket I have made some constraint. The orientation of peptides are similar. 

Post Situation: 

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