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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: 

reporting bugs? (erraser in rosetta 3.10)

Category: 
Compilation

Hi,

Is this the right place to report bugs that have appeared in erraser?  If not, could someone point me to the correct location?

These appear to be occuring in the rosetta 3.10 release (some in python code, others appearing to be in c++ code); and do not appear in erraser from rosetta 3.7; and occur when using the demo example from https://www.rosettacommons.org/demos/latest/public/erraser/README.

 

Best,

Pete

Post Situation: 

Model truncated proteins

Category: 
Structure prediction

Dear all,

I just started to use Rosetta and I am trying to model my protein with truncated sequence (First ~200 aa). I have pdb file of the full sequence and I would like to know the structure will look with first ~200 aa. Which protocol is better for me to use? Comparative modeling or Ab initio modeling? I am also curious about what that input native proteins is doing? Should I just provide my full sequence pdb file?

Post Situation: 

Regarding snugdock Ag-Ab score

Category: 
Docking

Hi There,

I am running snugdock locally for an Ag-Ab complex.  Program is running fine but I am getting all score value 0.00.

SCORE: total_score         rms CAPRI_rank       Fnat       I_sc       Irms   Irms_leg atom_pair_constraint                cbeta              cen_rms chainbreak complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA

Post Situation: 

ddG calculations to study point mutations

Category: 
Scoring

Hi,

I am using Rosetta protocol to determine ddG changes on point mutations in a peptide bound to a protein complex. I first used FastRelax to remove any steric clashes in the protein structure and then ran the ddG protocol to generate ~1000 structures till there is no change in ddG values. I now want to build a correlation plot between the Rosetta ddG values and experimental calculations.

Post Situation: 

Threading with Ligand

Category: 
Structure prediction

Hi everyone,

I'm trying to use the partial_thread application to fill in some gaps in a PDB crystal structure, 2hko.  This structure has an FAD ligand and a key water I'm trying to keep during threading.  I've cleaned the file as recommended, changed the FAD ligand atom types to match the canonical Rosetta atom types, and made similar changes to my water.  While the threading runs, the ligand gets thrown out.

This is the command I used:

Post Situation: 

Weighted scores??

Category: 
Structure prediction

Hi all,

Recently, I used the one point mutation on Rosetta Backrub server for getting predicts of mutation.  What I got are weighted scores after calculations.

My questions are 1.) what's the units of these weighted scores?

2.) what's the relationship between weighted scores and delta delta G (delta G of mutation - delta G of wild type)?

3.) In the output file, these weighted scores (total) are positive for both wild type and mutation. Are they correct? 

I'll appreciate for any help from you.

 

Post Situation: 

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