The problem hasn't been solved
Hi
I am trying to model c terminus of my protein while keeping the majority of N terminus structure fixed. I an using broker domain insertion for this purpose. in the domain_insertion.xml file, I need to provide topology file for my protein. How can I make the topology file?
Thank you
Dhiraj
Hi
I am trying to model missing C terminus of my protein using FloppyTail. I have experimental data regarding the radius of gyration that I want to use as constrain to narrow down the search space. How can I put that constrain?
Thank you
Dhiraj
Hello Everybody,
I'm using Rosetta to find a sequence that fits a given main chain using the fixBB or the PackRotamersMover. What I haven't been able to find out: How do I tell Rosetta to use the amino acid, which was selected by the alorithm for position X, also at position X+Y? In other words, the sequence should be identical at positions X and X+Y, but I would like to leave it to Rosetta to select a suitable residue and find suitable rotamers.
Thanks for your help.
Hello
I am trying to compile rosetta_src_2017.45.59812 using gcc-5.5 on a centos machine.
First of all,
./rosetta_compiler_test.py /home/ertinaz/gcc-install/gcc-5.5.0/bin/g++-5.5
gives
Summary:
Main Tests: 16 of 16 passed
Optional Tests: 5 of 6 passed
REGEX: <<<FAILED! (Compiled but did not run.)>>>
First question is which gcc version would pass the entire test?
HI
I am performing a local docking using Rosie server for a complex obtained from patchdock. The residue names are checked as in Rosetta nomenclature. But strangely the resulting pdb shows a missing residue, that is the first residue of both the protomers are missing. How is it possible or how to overcome it?
Hi,
I want to use snugdock in Rosie to model the binding structure between an antibody and an antigen. This is my input: http://rosie.rosettacommons.org/fs/46862/input/proteins.pdb
I get the following error message:
Hello everyone,
I want to draw your attention that I am failing to build PyRosetta on the new Ubuntu 18.04 (released last week).
My setup:
I build as per the documented method (which works in older Linux versions):
But I get the following error:
Dear Rosetta Users,
I am trying to design a loop present in a protein-protein interface. At the end of my design protocol, I inserted a LoopAnalyzerMover to assess the output decoys. To my dismay, I find very high LAM score, for all loop designs. An example LAM output is below:
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
I'm doing denovo density prediction. I wonder if the denovo_density can handle the presence of extra densities or the absence of denisties in the map? Would it try to fit the structure in all of the densities provided or just the relevant density? Does it undo wrongly placed fragments in more advanced iterations?
Thanks.
Hi,
I am using Rosetta 3.8 and trying to use the CartesianMD mover in a RosettaScript. This is what I put in the MOVERS section:
<CartesianMD name="md1test" scorefxn="talaris2014" rattle="true" scorefxn_obj="talaris2014" nstep="1000" temp="300" premin="50" postmin="200" report="20" report_scorecomp="1" selectmode="minobj" />
And after running with some general input options it gave me this error message:
Error: Element 'CartesianMD', attribute 'scorefxn': The attribute 'scorefxn' is not allowed.