The problem hasn't been solved
Hi there:
I am working on antibody engineering and have couple of questions about SnugDock function in ROSIE.
Mac OS Catalina 10.15.5
Python 3.7
MinSizeRel.python37-258
Hello, I am having trouble setting up PyRosetta after it is installed on my computer. I have unpacked it but when I try to do - cd setup && sudo python setup.py install - in command line it asks for a password. The password I was given with my academic license does not work. Any help or guidance would be much appreciated.
Hi, I am using mol-to-param script to generate param files of my conformer. the sdf file looks normal before generation. But the PDB looks weird with some bonds connected to each other when I visualize it in pymol software however it looks totally fine in chemdoodle3D. Anyone has any clue about this?
The PDB with weird structure looks like this:
Hello,
I am receiving the following XML validation error when implementing OptimizeMembranePositionMover:
Error messages were:
From line 11:
Error: Element 'OptimizeMembranePositionMover': This element is not expected.
Hi all,
I've recently been asked to try to use RosettaScripts for some enzyme design. In this particular case I am trying to use the HBNet mover to predict hydrogen bond network mutations. I have created scripts with just the HBNet mover and also calling the Multiple Pose mover afterwards. However, I am having the same issue. I don't know how to score the resulting binary silent file.
I am trying to select the top 5 results and extract their PDBs.
Some common errors include:
Dear Sir and Madam,
When I run such a script "~/rosetta_src_2020.08.61146_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -parser:protocol Design.xml -s some_relaxed_protein.pdb -database ~/rosetta_src_2020.08.61146_bundle/main/database/ -restore_talaris_behavior true -remodel:use_pose_relax true -score:set_weights pro_close 0 cart_bonded 0.5 -nstruct 10 -out:prefix design_" for insertion one amino acid, replacement one original amino acid into another and building additional disulphide I meet with the following error:
"[FILE]: SIGSEGV
I've run into an issue building a model using denovo_density in step 4D of this protocol: https://faculty.washington.edu/dimaio/files/rosetta_density_tutorial_aug18_4.pdf,
The rosetta command that throws the error is:
I saw there was a release that's compatible with py3.8 but the links for Mac versions lead to a "Not Found" page and there aren't any links for this version in the archive either. Not sure if that's an issue on my end or there was an upload issue.
Dear all,
I am trying to running RAbD with the following command:
antibody_designer.linuxgccrelease \
-l design_input.list \
-primary_cdrs H3 \
-graft_design_cdrs H3 \
-seq_design_cdrs H1 H2 \
-do_dock \
-paratope H3 \
-mc_optimize_dG \
-mc_total_weight .001 \
-mc_interface_weight .999 \
-out:path:all designing\
-out:file:scorefile designing_scores.fasc\
-nstruct 3 | tee designing.log
Hi, I'm trying to use simple_cycpep_predict to model the conformation of a disulfide linked cyclic peptide. The peptide has an amidated C terminus. I've been trying to get the patch Cterm_amidation working however it appears to ignore the patch.
A sample input sequence is:
CYS ALA ALA ALA ALA CYS ALA ALA ALA:Cterm_amidation
And here's my test input script: