Could someone shed light on -detect_disulf_tolerance ?
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:
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.
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?
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.
Please let me know the best way to go about this. And many thanks.
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
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...)
I'd like to fold-and-dock a trimeric transmembrane domain. I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/. However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards). I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock". Is this possible, and how do I do it?
I'm folding a protein which is a trimeric long helix bundle. I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc). This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves. I'd like to constrain this to extended conformations only.
I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:
One step in RosettaCM is
partial_thread.default.linuxgccrelease -in:file:fasta JN254802.fasta -in:file:alignment JN254802_5tx1.grishin -in:file:template_pdb 5tx1_clean.pdb
But there are more than 9999 residues in the JN254802.fasta. The output "5tx1_clean.pdb.pdb" writes residue number 10000, 10001, 10002, etc as 1000, because only four positions are allowed for residue numbering (see the example in the end of this post).
