The problem has been solved
Hello, I am very new to PyRosetta, so this might not make a lot of sense. What I'm trying to do is minimise the energy of a given pose. I don't know much about this, so any tips about how to approach it and which instruments to use would be appreciated. Thank you.
Dear Ligand binding Team,
I am writting this letter of appreciation to thank the team of Rosie Ligand Docking for making available such a powerful docking tool for researchers. We recently used the tool and got wonderful results using a difficult protein (oxidosqualene cyclase). We also want to thank you for making rarely available docking tool based on Induced-Fit freely available to academic users.
We hope that you continue providing the Rosie tools and keep updating the excellent Ligand Docking tool.
I want to use RosettaCM for density guided homology modeling. My structure contains taxol and other ligands: GTP and GDP, but my /rosetta/main/database/scoring/score_functions/facts contains params files for just GTP and GDP but not taxol. I atatched my taxol.pdb file for reference.
Thanks in advance.
Hello Rosetta devs,
I'm not sure that this is the right place to post a bug. If not, please let me know where to post.
I compiled both Rosetta 3.10 (and then 2019.07 release), and faced the following error when trying to predict cyclic peptides with terminal disulfide bonds using the simple_cycpep_predict protocol.
To be more specific, my peptide has a non-terminal CYS residue at the C-term, and I was using the
Hello everyone,
I am reading about the Abinitio protocol to see how I can include a checkpoint file in the Abinitio flags, but i could not find any information on how to input a checkpoint file. so this is my question:
I've been trying for a while to build Rosetta on a cluster.
I'm getting errors related to sqlite3.c. Does anyone know how to fix this?
Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro. Thanks in advance
</SCOREFXNS>
<FILTERS>
Hi everyone,
I wanted to let you know about a bug that I was able to fix. if you use the make_fragments.pl in the /rosetta/tools/fragments/ folder it calls another script install_dependencies.pl it calls an online script update_blastdb.pl which in the install_dependencies.pl is at this url:
https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl
it returns a 404 error.
Hello everyone,
recently, i doing the Exercises of workshop6, but i found i was confused about the packing and design in rosetta...
Anybody can help to figure out why the two setting method of PACK （def pack1 and def pack2) return different energy？it should be the same as i think！
if i run pack1 followed by pack2, then it return the same(lower) energy. it seens that the design energy is not optimized. so should i set another packing after the design?
thanks if anyone can help.
MY CODE: