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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: 

C-termini remodelling of dimeric structure removes second chain

Category: 
Loop Modeling

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:
-in:file:s bestp1.pdb
-remodel:blueprint c-term.remodel
-no_optH false
-ex1
-ex2
-remodel:num_trajectory 1
-remodel:quick_and_dirty

Post Situation: 

Installation of Rosetta on Mac BigSur

Category: 
PyRosetta

Hi, 

 

I have installed pyrosetta and rosetta on my system and when I try to import in my python code it says module not found. I have a BigSur mac computer. Is it because of my system? Can someone help me who has also installed it on bigSur?

Thank you in advance!

Best,

Rashmi

 

Post Situation: 

Help with file in article Kemp elimination catalysts by computational enzyme design

Category: 
Design

Hello, I would like to ask for some help, regarding the article Kemp elimination catalysts by computational enzyme design, you would still have the transition state calculated by gauss, I need the output because I am trying to replicate the article, and I need the coordinates of the hydrogen being removed from the carbon in the transition state. Does anyone have these outputs?

Att. Thank you

Post Situation: 

Linker Building in scFv

Category: 
Loop Modeling

Dear Rosetta Users, 

I would like to build a linker that connects the VH to the VL domain of a single-chain Fv.
The length of the linker is ~15 aa (actually I'm going to build two linkers which differs in term of length).

In the literature, I found a case in which the RosettaRemodel application was used to perform a loop closure with a glycine-serine linker between two domains.

However, the sequence of my linker is known and it must not be changed. 
I just need to build -and not design- the linker.

Post Situation: 

farfar2 error

Category: 
Structure prediction

Hello

I am trying to model a 514-nt long RNA structure using farfar2. My job failed with the following error

ERROR: Not complementary at positions A    8 and U   13

I do not understand this, A and U are complementary  and I have checked both the input sequence and dot bracket files and I dont see any discrepancies. Attaching both inputs and the Rosie crash log file. Could someone please help me sort the error.

Thank you

Post Situation: 

Stepwise error

Category: 
Nucleic Acids

I am getting the following error while trying to assemble a 514-nucleotide long RNA using the "Stepwise" programme:

"one of your input pdbs -- native, alignment, or starting -- has a residue that is not found in the fasta!"

I have thoroughly checked my target fasta sequence  and the input PDB containing part of the RNA structure. There are no residue mismatches...then why am I getting this error?

Post Situation: 

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