The problem hasn't been solved
Hi,
I downloaded the 2016 linux release of Rosetta3 (rosetta_bin_linux_2016.32.58837_bundle) about 6 months ago. I have just now found that the partial_thread.default.linuxgccrelease executable needed for RosettaCM is missing. Is there any particular reason why it would not have been built? How do I fix it?
Thank you,
Claire
Hello,
I have been trying to use mr_protocols on a homologous pdb into a cryo-em density. When I run the protocol with symmetry and without the ligand it works properly. The trouble comes when I try to include a ligand. The resulting pdb is does not contain the ligand. This is the mr_protocol that I have submitted:
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#!/bin/bash
I am having some difficulty applying Relax using the prebuilt Rosetta 3.7 on TACC:
Hi,
I would like to reproduce the score graph that is shown after the job has finished. For this I would need the score values and the RMSD but in the score file I can only find the RMS. Does anyone know how I could get the RMSD values?
Thank you in advance!
Laura
Hello,
I relaxed the homodimeric biological assembly of PDB 1ISA, and am trying to use Interface Analyzer to calculate the interfacial energy between the subunits. I have cleaned the strucutre to removed all the water, metals, et.c and leave only the protein residues. Below are the command line flags I am using:
In the prepack folder after a successful docking2 run, I have three PDB files:
proteins_prepacked.pdb
proteins.pdb
proteins.prepack.pdb
Why? Which one is the prepacked structure? And, why is prepack_score.sf empty?
SEQUENCE:
SCORE: total_score description
SCORE: 0.000 proteins_0001
[All output files attached.]
Is Docking Prepack simply a specialized version of Relax for dealing with complexes? (separate complex, minimize sidechains, reassemble)
If I am docking proteins A and B where each has already been individually relaxed, is there any need for running Docking Prepack on the PDB file that contains both relaxed A and B, already oriented correctly for local docking?
Dear all,
I am using the fragment picker for multiple peptides. The issue is that I am using a limited vall library. Is there a way to produce an updated vall library from PDB or the Robetta server? I see that Robetta fragment files are available here: http://robetta.bakerlab.org/downloads/casp/casp12/fragments/ . But is there a way to combine them into a vall file?
Thanks in advance,
Alex
Hi,
I want to use https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Filters/filter_pages/DeltaFilter to calculate the difference in energy between wt and design. I think I have to use parameter relax_mover, but from the docs It is not clear what value to use. Does anyone have any experience with it?
Edit:
I dug into the source code and it appears that this should work:
I was following the antibody modeling tutorial on Nature Protocols paper and I wasn’t successful. I followed the tutorial in the Supplementary Material, and got the following error right after performing blastp query. Blast+ was performed well and produced output alright.