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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

selecting pivot_residue in Backrub for ensemble generation

Category: 
Docking

Hello,

I need to generate an ensemble of proteins to capture backbone flexibility in docking. I ran relax with thorough flag, but the resultants decoys are not that much different (RMSD ranges fro 0.2 to 0.7). Then I ran Backrub without defining pivot_residue and without resfile. The resultant decoys of Backrub are also similar. Does anyone have suggestions to define pivot_residue? or how can I sample conformational space enough to consider backbone flexibility?

 

Thanks

Post Situation: 

how to know the precedure of solving a actural bio problem? like interface design?

Category: 
Design

hi 

im a doctorial student in the learning process of rosetta scripts

and i was to solve a problem like i got to design a protein complex A0_B0 with known structure and known complex of A1_B1 A2_B2 all Bi are homologs

i need to design a binder A0 that binds to B0

but I just dont know how

and a teacher told me that i needed to manually docking B0 to like a1

and to use fastdesign,fastrelax, to use taskops of layerdesign,limitaromachi2,PruneBuriedUnsats,and filters like BuriedUnsatHbonds

Post Situation: 

Bug Report - Encoding issue

Category: 
Design

I had to do a hard shutdown of a workstation while remodel was running (mpiserialization, openmpi) and when it booted up, i ran remodel again. It had no issues running but checkpoint.txt has a different encoding now like this:

I have no idea why or how, but i purged and reinstalled gedit and it stays the same. I also tried vim and it doesnt display the checkpoint number properly either. It doesn't bother me at the moment, but might be worth checking out why it happens.

Post Situation: 

mpirun docking_protocol

Category: 
Docking

Hi all,

I was running mpi docking_protocol (docking_protocol.cxx11threadmpiserialization.linuxgccrelease) to generate 500 decoys. I got this error and only 470 decoys as output:

[ ERROR ]: Error(s) were encountered when running jobs.
12 jobs failed;
Check the output further up for additional error messages.
---------------------------------------------------------------

Post Situation: 

Controlling Input in the Tutorial

Category: 
Scoring

Hi All,

I am trying tor learn Rosetta basics using the tutorial https://www.rosettacommons.org/demos/latest/tutorials/input_and_output/input_and_output 

However, when I try like it is instructed in the tutorial following error happens:

Infinity4s-iMac-2:main smbatgevorgyan$ cd demos/tutorials/input_and_output/

Post Situation: 

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