The problem hasn't been solved
I'm trying to create a threaded model according to this tutorial: https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM
I'm not sure why I'm getting this error, how to debug it?
Hi all, I'm trying to run relax on a pdb which has ACE and NME terminal caps. Is there a way I can preserve those in the output? I'm not an expert Rosetta user, but here are some more specifics of what I've tried:
Hi, is there a way to use Robetta for creating fragments for short peptides?
Currently, there is a minimum length of 27 required.
Cheers, René
I have a scenario where a protein is composed of two domains (its actually two chains, but I can make it a single chain) for Rosetta's purposes.
Hello everyone,
I wrote a forum entry here (https://www.rosettacommons.org/node/10258) asking about details on RosettaDesign, and I am continuing the conversation here since I ran my script on several structures and got different results and I want a better understanding.
Please find attached a summery of the results. If you look closely you can see the green relaxed structure on the bottom left (sorry if it is not clear).
I am trying to run the cartesian_ddg protocol (https://www.rosettacommons.org/docs/latest/cartesian-ddG).
I am using the following command:
cartesian_ddg.static.linuxgccrelease \
-database $ROSETTADB \
-s min_2b5i-A_0001_clean_0011.pdb \
–ddg:mut_file themutfile.txt \
-ddg:iterations 3 \
-ddg::cartesian \
-ddg::dump_pdbs false \
-bbnbr 1 \
-fa_max_dis 9.0 \
-beta_cart
Can anyone point to how the rama score is evaluated for ALL residues in a given run by a Rosetta application?
I have been looking through the src/core/scoring/Ramachandran* and src/core/scoring/methods/Ramachandran* code pieces and see in most places only the individual residue measurements ( eval_rama_score_residue() ). There is a void function in Ramachandran.cc that goes through all residues (eval_rama_score_all() ), but this function is not called in any of the protocols or applications in Rosetta.
According to the Rosetta density tutorial:
"Generally, we select the best 20% of models by geometry, and selecting the best overall by free FSC. The top 5 models should be inspected for model convergence as well as visually inspected for density map agreement"
I would appreciate if someone explains why we choose the lowest FSC score, and what does it mean to have a negatrive FSC score? Also, according to the paper quoted below, shouldn't we sample for the highest free FSC and bnot the lowest?
Hello!
I am using the standalone version of Rosetta, and so do for the Fragment picker application. in the tutorial, 3 SS prediction programs are used with weightage of 0.6 for psipred and 0.2 each for other two programs; however, the Robetta server, produce results based on only 02 programs, i.e. psipred an Jufo so in this case, what is the weightage for both programs?
Thanks!
Malkeet