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constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)

Category: 
Constraints

Hello,

I am performing Rosetta ligand docking for an enzyme A to a ligand X which should be covalently bound to a small protein B.  I need to impose this covalent bond and some other catalytic constraints (distances between ligand and receptor's residues and also the distances between two residues of the receptors )  to my ligand docking.  I  found several movers for adding constraints including AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover, but I am confused about which one works with Rosetta Ligand docking. 

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[Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence

Category: 
Structure prediction

I am trying to run RosettaAntibody3 to build an Fv hhomology model from an input sequence. I am following the documentation form here.

I am using the command: 

antibody.static.linuxgccrelease \
  -database $ROSETTA_DATABASE \
  -fasta /mnt/data/input/myinput.fasta \
  -nstruct 1 \
  -out:path:all /mnt/data/output/output-graft/ \
  -detect_disulf false

 which fails fairly quickly with the error:

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Error compiling mpi under Big Sur

Category: 
Compilation

Using updated Xcode and a fresh install of macos Big Sur, I get the following error (below) when compiling using: "./scons.py -j 12 mode=release bin extras=mpi"

 Open-mpi is installed (via homebrew) and if I run "ompi_info" all the info seems correct (see atached .txt). Any suggestions would be appreacited. Thanks!

-Andrew

 

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De novo backbone trace from fragments

Category: 
Structure prediction
Design
Loop Modeling

Dear Rosetta experts,

I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.

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How do I insert or delete residues into specific locations?

Category: 
PyRosetta

I want to insert/delete residues in sequences. My goal is to take mutant sequences, have them become similar sequences of the WT and focus on each mutation. Is that possible?

 

Example: ABABA, and I want to insert "C" into the third position so it would look like this ---> ABCABA

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protein-ligand docking rescoring with interfaceAnalyzer

Category: 
Docking

 Hi 

 My name is Jong hui Hong

 I'd like to rescore docking result structure made by Rosetta-script application with InterfaceAnalyzer

 But InterfaceAnalyzer application binary couldn't be found in binary folder ( rosetta-source/main/source/bin) .

 Is there any other folder for that application ?

 It seems that InterfaceAnalyzer source is there in Rosetta source

 Can there be something wrong with my rosetta installation?

 Any kind of suggestion or answer would be appreciated 

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