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Scoring correlation with electron density map

Structure prediction

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 ./ -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"

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Changing amino acid profile while keeping the backbone conformation between 2 protein structures (need help)


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. 

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Intel MPI: early exit due to job process stopped.


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:

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Calculating SAP score using RosettaScripts



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.









        <PerResidueSapScoreMetric name="sapscore"/>


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Set torsions for atoms in different residues

Non-Canonical Peptides

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:

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Simple_cycpep_predict with crosslinker BBMB

Structure prediction

Hi all,

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.

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