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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

use_truncated_termini not working in combination with params files

Category: 
Structure prediction

When using FastRelax with the keyword -use_truncated_termini true as expected no OXT are added if not present in the input file. However, when I run the same protocol with additional params files (-extra_res_fa), OXT are added to all chains and the -use_truncated_termini seems to be ignored. Does anyone know/suspect a reason for this and might know a workaround?

Thanks,

Georg

Post Situation: 

Docking of multichain oligomers

Category: 
Docking

Hi all,

I'm trying to perform docking simulations for two identical coiled-coil homodimers modelled by the fold and dock protocol to establish the potential ways of interaction of these in higher order complexes (there's an experimental evidence for the formation of such assemblies).

 

The command looks as follows:

docking_protocol.linuxgccrelease -in:file:s S_029104.pdb -unboundrot S_029104.pdb -nstruct 1  -randomize1 -randomize2 -ex1 -ex2aro -partners AB_AB 

 

Post Situation: 

Is a bash command "wget" a reasonable way for download of Rosetta with binaries?

Category: 
Compilation

Dear Sir or Madam,

previously I have always downloaded Rosetta with binaries. But for now the Rosetta package with binary files became too huge (over 17 GB), which makes the Rosetta package download through slow browser (1 Mbps in average and it doesn't depend on a browser) really complicated deal. Other problem, which complicates downloading the Rosetta package, consists in that, what the download process is aborted when laptop screen fades and laptop go to sleep mode.

Post Situation: 

SARS-CoV-2: call for compound predictions against protease

Category: 
Small Molecules

There is a recently set up call for compound suggests that may be active against the protease SARS-CoV-2, the etiological agent of COVID-19.

Diamond lightsource XChem team did a fragment screen against it and released last week with many hits, which are starting points for designing the next round of compounds.

Post Situation: 

Breaking fastDesign into more stages or writing something custom

Category: 
Design

I know that rosetta_scripts XML protocols can be run in PyRosetta, and I think there is also a specfic PyRosetta version of fastDesign.  But I'm wondering to what extent the underlying functions used in fastDesign (e.g. modifying constraint strengths, modifying vdw repulsion terms) can be written in PyRosetta directly such that some customization would be possible?

 

Post Situation: 

application for affinity optimization

Category: 
Design

Hello

Which application is suited for increasing affinity between 2 proteins? I would like to specify ranges of residues to be mutated in only 1 of the proteins/chains, e.g. in a resfile. 

Essentially I want to do something like the opt-dG application in RAbD, but with ranges of residues a protein domain that is not an antibody. Can the opt-dG do this?

Post Situation: 

Rosetta compilation error through newer gcc-g++ versions

Category: 
Compilation

Dear fellows,

I have recently downloaded and untar new version of Rosetta - as a rosetta_src_2020.03.61102_bundle folder. When I tried to compile it via standart command "./scons.py -j6 mode=release bin" in /main/source/ directory, I got such error:

"g++: warning: switch '-ffor-scope' is no longer supported

Post Situation: 

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