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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: 

Rosetta_cm Partial Threading Removing Parts of Sequence

Category: 
Structure prediction

Hello,

I am currently trying to homology model the PAR1 receptor with the P2Y12 receptor as my template structure, but for some reason I believe that parts of my sequence are being altered/removed, namely the loop regions.

For example, the original PAR1 sequence is as follows:

Post Situation: 

Mutations are ignored (fixbb) when using -auto_setup_metals option

Category: 
Design

When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).

Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals

Post Situation: 

Ligand-protein complex, ERROR: LOWER_TERMINUS_VARIANT

Category: 
Design

Hi all, 

I am working on an enzyme that happen to have a Methionine to be one of its ligands. I generated a params file with mol_to_param script. And I have done the following to read this params file.

params_path = Vector1(['MET.params')]

pose = Pose()

generate_nonstandard_residue_set (pose, params_path)

pose_from_file(pose, 'struct.pdb')

Post Situation: 

Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for a protein-protein docking

Category: 
Loop Modeling

Dear Sir or Madam,

I got a one complicated problem, which took place during loop modelling for protein-protein docking. I carry out tasks from the Meiler tutorial for Rosetta.

Post Situation: 

VH-VL Orientation in antibody

Category: 
Structure prediction

 

How to determine the VH-VL orientation angle in rosetta. i came across this manuscript "Improved prediction of antibody VL–VH orientation" by Protein Eng Des Sel. 2016 Oct; 29(10): 409–418. Here there is description of MT protocol. Whether the script is provided in the rosetta 3.1 version. Or is there any other alternative in rosetta to calculate the VH-VL orientation (LHOC) angle of antibody in rosetta.

Post Situation: 

Rosie vip function fails on multiple tries

Category: 
Design

Hi:

 

I can not get the rosie server vip function to complete.  After many hours it always ends with

 

VIP Job vip put cds 81q1 prepared pdb 「№72207」 Details

 

this error :

 

Job 「№72207」has failed with the message:

JOB FAILED: Scripts failed to produce HPC jobs json file...

 

Have tried several times now, thanks for any advice

 

- Amy F

 

Post Situation: 

Updating databases and weekly update

Category: 
Compilation

Hi,

I already have rosetta compiled in my linux workstation and it is working fine. Few questions regarding  regular updating of databases. How should I update the databases of rosetta. I know that there are weekly release for rosetta updating these release is enough. whether the weekly release has all the relevant updated database.   How  do I update the rosetta. Whether I have to recompile the source code from the weekly updates. These are very basic questions and your response will be greatly appreciated.

Thanking you

Post Situation: 

Enzyme Design FlexBB Protocol Bug: DNA/RNA handling

Category: 
Enzyme Design

Hi Folks,

I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default  protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA  in the pose triggers the following error consistently after cst minimization. 

Post Situation: 

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