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I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:
"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"
Hello, i am a masters student trying to play around with rosetta. And i have a project in mind. I have two protein structures: nanocages. each with 60 monomers but the chains are a little bit different with different aa profiles. Now what I want to do is to make a structure with the backbone conformation profile of one of the nanocages but with the amino acid profile of the other one. How do i go about doing this? I'm sorry if I wasn't clear english is not my native language.
Thanks for your help in advance.
Hello, I am using rosetta docking_protocol compiled with Intel MPI (from Intel® oneAPI Toolkits 2020), and I have some problems / bug reports.
I requested 3 output poses with '-nstruct 3' and I ran 'mpirun -n 3 docking_protocol.mpi.linuxiccrelease ...' to start one master rank and two slave ranks. However, when one slave (rank 2) finished its jobs and master will send spin down signal:
I am trying to calculate the per residue SAP scores of a protein structure using Rosetta scripts. The .xml script I am using is shown below.
I am working with a polymer with a non-aminoacidic backbone comprising two subunits, each defined as individual residues. I have already defined the params file for both subunits; however, I am experiencing issues exploring torsions between these connected residues. I am setting the angle movement using pose.conformation().set_torsion_angle(). This function has worked for angles between atoms inside the same subunit. However, when trying to set_torsion_angle() for atoms residing in different residues, I get the following error:
I'm trying to use simple_cycpep_predict with crosslinker BBMB, and the generated structure (see attached) does crosslink with BBMB. However, it also does a head-to-tail cyclization between the 2 termini and I would like to not have that happen. It's not clear to me from the help file how to do that as the default uses head-to-tail cyclization. Is there a way to turn that off?
Here is the sequence file, the parameters that I'm using, as well as one of the generated structures to illustrate what I am having issues with.