# Structure prediction

## RosettaCM: An internal error has occurred when "Running the Hybridize mover"

Category:
Structure prediction

Hello,

I am trying to replicate the tutorial for RosettaCM according to the following URL:

The step 1 (using setup_RosettaCM.py) is fine where I can obtain the thread pdb file and flags and rosetta_cm.xml.

But when I tried to run step 2 (Run the Hybridize mover). It crashed.

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## The difference between the H1 regions of modeled camelid antibody and the crystal structure.

Category:
Structure prediction

Dear all,

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## "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease

Category:
Structure prediction

Dear all,

I am trying to modeling a camelid antibody with the sequence (nb.fasta) as following:

\$cat nb.fasta

>heavy

I use antibody.linuxgccrelease to model it:

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## Problems with mpi version of antibody.linuxgccrelease

Category:
Structure prediction

Dear all,

When I run the "antibody.mpi.linuxgccrelease", like

antibody.mpi.linuxgccrelease -fasta vhh.fasta -vhh_only | tee grafting.log

I always get the following strange information when the program approachs finishing and all grafted models have been produced:

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## The usage of antibody_H3.linuxgccrelease

Category:
Structure prediction

Dear all,

I am trying to use the antibody utinity to modeling a camelid antibody (vhh). I used the antibody.linuxgccrelease to produce 10 relaxed models for this  vhh sequence. Then I moved to do the H3 modeling. The "antibody_H3.linuxgccrelease --help" command shows many options for the antibody_H3.linuxgccrelease. However, I am a bit confused about the antibody_H3.linuxgccrelease options.

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## RosettaAntibodyDesign: How can I run the protocol without allowing design?

Category:
Structure prediction
Docking
Design

Hi there,

I am trying to use RosettaAntibodyDesigner without allowing any design elements of the protocol to occur. I understand 100% that this would remove the intended purpose and use cases of RAbD, however, I am trying to piecemeal a side-by-side comparison of a designed mAb (which works reat through this protocol) and a non-designed mAb.

However, I would like to ensure that both my simulations are executred identially otherwise. (ie., loop flexibility in docking, etc).

Is there any way to runn RAbD while FIXing all the CDRs?

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## Modelling temperature dependent RNA structures

Category:
Structure prediction
Nucleic Acids

Hi to all,

I am really new to rosetta. I am using rna_denovo to generate 3D structures of RNA. I believe the default tempertaure used for modelling is 300K. I want to know if we can set our own temperature  for modelling RNA ? I did saw the option of temperature in the -help, written as 2 in the settings option, but I am not sure how to use it. Can we just define the temperature that we want, after writing this option? I am not sure how to go about this.

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## RosettaAntibodyDesign] How can I use run_relax and run_snugdock as part of my command and workflow?

Category:
Structure prediction
Docking

I am trying to run a basic antibody/antigen design/dock simulaton using RosettaAntibodyDesign (from Rosetta 3.12)

I am using the command:

antibody_designer.macosclangrelease \
-database /path/to/database/ \
-do_dock \
-use_epitope_constraints \
-nstruct 5 -in:file:s complex_renumbered.pdb \
-seq_design_cdrs H1 H2 H3 \
-primary_cdrs H3 \
-mintype relax \
-run_snugdock \
-run_relax \
-out:path:all ./output 

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## How to fold-and-dock in PyRosetta?

Category:
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3)

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

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