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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.
I am trying to design a 2 fold-symmetrical protein where I want to design a selected number of residues in each half and not mutate the remaining residues in both the halves. For e.g., what I want Rosetta to do is in "Half-A, the residues at position 32, 49, 56, 65, 66 should be mutated to certain residues, and the exact same mutated residues should appear after designing position 32, 49, 56, 65, 66 in Half-B.
I have used ROSIE server to analyze protein-antibody interaction and predict peptide sequences of antibody that would interact with the protein.
The analysis revealed 3 hotspots of the antibody sequence as in the picture attached. It did make sense to me that the predicted linaer peptides from antibody sequence were chosen from 1st and 3rd hotspots from the figure with highest contact points with the protein.
Dear caretakers/kind strangers,
I ran into an error that i do not understand when trying to do de-novo modelling of a helix linker using REMODEL. When i leave the blueprint file without any new residues it runs fine. But when i add new residues at the end (C Terminal) the program recognizes it is a C terminal extension, but throws this error.
I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error:
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.