The problem hasn't been solved
Dear all,
I have a antigen-antibody complex, and I wish to design the antibody in antigen-antibody interface in order to remove crash and improve affinity. Could anyone tell me what is the most direct way to do this.
Thank a lot!
I have written a script using PyRosetta (pyrosetta-4.0-py2.7 retrieved from github 2017-05-23) which:
- imports a PDB file containing a full antibody structure and antigen dimer separated by around 100A
- defines a custom fold tree with the Fc at the root and a jump edge connecting the Fc to the antigen
- creates ambiguous site constraints consistent with interaction of variable loops of the two Fab domains with the epitope of each antigen in the dimer
Hi,
I have been trying to write a custom energy method class following the workshop #11 from the Gray lab and this tutorial http://graylab.jhu.edu/pyrosetta/downloads/scripts/test/T850_SubClassing.py . Here is what I have:
Hi everyone,
I downloaded the rosetta package for linux (version 3.8). During the compilation I receive an error saying:
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 102: ordinal not in range(128)
scons: building terminated because of errors.
Can someone help me to resolve this problem. Thank you.
Dear all,
I have a pdb file which contains three chains (A, B, and C) for a protein molecule. According to my knowledge, the protein should be 3-fold symetric and a trimer of the three chains. Is there a way to generate the pdb file which contains all the 9 chains for the whole molecules? I can only find some infomation from the original pdb file about the symmetry like these:
Dear all,
recently I have tried to dock some different peptides to binding pocket of protein kinase and see their performance in flexpepdock. In the meanwhile I also dock some random peptides, such as poly G (GGGGGSGG) and poly E peptide(EEEEESEE). Interestingly, the energy score of good peptides and random peptides didn't show much differences(from -650 to -690), sometimes the random peptides even showed the better energy score. In order to keep them in the pocket I have made some constraint. The orientation of peptides are similar.
Hello,
I have a question about KIC protocol. I am using the next generation protocol together with fragments. I think it should be fine but I just wanted ti double check couple of things.
Firstly, can I use fragments together with these flags? :
-loops:taboo_sampling
-loops:kic_rama2b
-loops:ramp_fa_rep
-loops:ramp_rama
-loops:kic_omega_sampling
-loops:allow_omega_move
Hello!
- I tried fix_bb script and used a resfile > 1 A NATAA, 2 A NATAA and so on as per sample resfile but it shows an error "core.pack.task.ResfileReader: On line 2, the chain identifier 'NATAA' must be just a single character in [_A-Za-z] (note the chain identifier is case sensitive)." I could not understand it.
Hi,
I'm just wondering, is the CASP local Distance Difference Test implemented in Rosetta?
I'm using "rosetta_src_2017.36.59679_bundle". I'm trying to fit some strucutres to an EM density map. My script exited with the below error. Please help me troubleshoot it and let me know if you need further details.
This is the script that's I'm running: