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I am trying to use MotifGraft mover to graft an epitope to a scaffold protein (actually there is a structure library, parsed with -l list).
The xml script is attached.
My command line is as follow (I am first trying a very loose boundary conditions, I'm aware about the higher RMSD/atom_clash values):
I'm trying to to use rosetta design (http://rosettadesign.med.unc.edu) to increase binding affinity between 2 proteins in 1 pdb file.
I want 2 residue ranges to be mutated in chain B but all other residues to remain the same. Therefore I have used this resfile:
71 - 88 B ALLAAxc EX1
50 - 56 B ALLAAxc EX1
However, the server mutates residues in both chains. How do I force it to only mutate chain B?
Using antibody_designer to graft loops on one CDR. I'd like to fix the sequence of the grafted loop to native. It appears to ignore the
I have tried something like this in my cdr_instruction file
H3 GraftDesign ALLOW
ALL SeqDesign FIX
I've also tried passing it a resfile forcing everything to be native like so
I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.
I have been using Rosetta design for quite a while but I did not pay attention to what Resfile header would do. I looked for descriptions and examples files different people have shared and used and I am unable to understand when I should specify NATRO or NATAA in the header?
I want to perform different tasks. For example:
1) Mutate specific residue to ALLAA and I use header like:
30 H ALLAA
whereas, I found someone using following header:
During single state design of protein the following error is encountered after relaxing the structure at the fixed backbone design stage and also by design iterated by backrub motion.
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job 4MUI_relax_design_0010
For outreach, I made a spinning and blinking FITC-labelled Christmas tree (https://michelanglo.sgc.ox.ac.uk/r/christmas) using various Rosetta tools, which I have learnt to use properly thanks to all of you.
So using the excuse of the cheer of the holiday season, I wanted to sincerely thank all of you for all the help I have recieved in this forum! It has been invaluable and I really mean it.