The problem has been solved
Where is the main website for PyRosetta?
Who is behind PyRosetta?
Where can I get PyRosetta?
If I have a Rosetta license, do I need a separate PyRosetta license?
Where is the PyRosetta documentation?
Are there additional PyRosetta FAQs?
Hello,
I have downloaded a PDB with a chemically bound ligand (small molecule)
I have followed (in every way that I can see) all the details presented in the tutorial/demo here:
https://www.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README
大家好！
我想为新底物设计甲基转移酶。该酶依赖于小分子作为甲基供体 (SAH)。因此，我使用 -extra_res_fa 参数将 SAH 包含为应用的输入。CST 文件包含三个约束：约束 1 涉及底物和 HIS 残基，约束 2 涉及底物和 ARG 残基，约束 3 涉及底物和 SAH。而SAH位于PDB的最后一个块。
I am still working on the Cao protocol. And I ran into another problem. When I ran step 15: Motif extraction. I ran the following command:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/fd_output_splits/xaa.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_
Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred:
basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176
Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred:
basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176
Dear ROSIE2 team,
thank you very much to making available such a great ressource.
I used the ROSIE2 server and AlphaRed to predict protein-protein interactions. While it works most of the time, I would like to share some of the error messages which I experience regularly. Maybe they help you to improve the software.
#####
AlphaRed job №16676
Hi,
I have a protien peptide complex and I want to design a peptide that will bind to the protein better the the WT peptide. What tools do you suggest I use? it can also be from
any of the other rosseta platform (or any other). My goal is to find 50 potential peptides and then test them experimentally.
Thanks,
Miriam
