You are here

Unsolved

The problem hasn't been solved

READ THIS BEFORE YOU POST

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: 

Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

Post Situation: 

New Python 3.7

Category: 
Compilation

Hello developers,

 

Just letting you know that there is a new python version (3.7) released and PyRosetta does not work in it. I use Arch based linux so I discover these things very early, just want to send you a notification here incase you feel you need to provide PyRosetta in python 3.7

 

I hope this helps.

Post Situation: 

ab initio struction prediction

Category: 
Structure prediction

hello

i want to predict denovo structure of a protein but at last step i get this error

opt/rosetta_src_2018.09.60072_bundle/main/source/bin/minirosetta.default.linuxgccrelease: error while loading shared libraries: libsqlite3.so: cannot open shared object file: No such file or directory

should i download libreries ? because i installed just rosetta with no library  please help me

Post Situation: 

recommended function type for cross links data

Category: 
Structure prediction

Hi,

I want to use rosetta ab intio with constraints from cross links data that I have, what is the best function type to put in the constraints file? 

Furthermore, what is the best function type for co-evolution data (from GREMLIN)?

Thanks,

Merav 

Post Situation: 

De novo density assembly weights don't add up to a 100

Category: 
Structure prediction

In the density guided de novo prediction script denovo_density.cc, there is this block of code here:

FragmentAssemblyMover::FragmentAssemblyMover() {
	overlap_wt_ = 4.0;
	clash_wt_ = 20.0;
	close_wt_ = 6.0;
	dens_wt_ = 0.85;  //fd

	if ( option[ assembly_weights ].user() ) {
		overlap_wt_ = option[ assembly_weights ]()[1];
		clash_wt_ = option[ assembly_weights ]()[2];
		close_wt_ = option[ assembly_weights ]()[3];
	}

	null_frag_ = option[ null_weight ]();
}

 

Post Situation: 

Relaxing protein-RNA complexes

Category: 
Nucleic Acids

I'm new to Rosetta and I'm trying to relax a model of protein subunits bound to a short strand of RNA into cryo-EM density. However, I keep getting bad input errors on the RNA strand when I run this through relax and I would really appreciate some help. I have similar problems when I run the clean_pdb script which suggests to me that I'm not providing rosetta the correct instructions, the coordinates and residue names appear to be fine when inspected manually.

Thanks and Best wishes,

Rob

 

Post Situation: 

Pages

Subscribe to RSS - Unsolved