You are here

Home

Unsolved

The problem hasn't been solved

How to add uncommon metal elements into Rosetta and make it recognizable?

Submitted by JasonIsaac on Thu, 2023-02-09 00:08
Category: 
Design

HI everyone, I want to RosettaMatch to introduce a ligand into a scaffold protein, but the ligand contains uncommon metals like Rh, I am afraid Rh is not recognizable like Fe by Rosetta. 

So I want to ask about how to add a new metal element to Rosetta, and how many files should I edit to make sure it's done? As far as I know, maybe I have to edit atom_type_sets and residue_types sets under database/chemical/, but more specifically, I have no idea.

Any suggestions would help!  And thanks for you time and effort.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Install pyrosetta on Ubuntu

Submitted by Xiao Zhu on Mon, 2023-02-06 07:02
Category: 
Compilation

I recently download the rosetta 2022.46 source code and rosetta 2022.46 ubuntu binanry. Then I'm confused how to install them. I try to unpack the binary file into my home directory, but then it seems nothing has been installed. for examle, "no module called pyrosetta" or "no module called pyrosetta.toolbox" or "init is not defined".

And I also complie the source code using scons , but it seems just create a bin folder contained release in some specific folder, but not installed in the system.

Who can help me to solve this problem?

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Score function in protein-protein docking with constrains

Submitted by Zehui Zhou on Mon, 2023-02-06 03:31
Category: 
Scoring

Hi, everyone!

I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:

a. Whether the ref2015  or ref2015_cst function considers the ligand (with params file)?

b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

No values for total score while running Rosetta score file.

Submitted by Shweata Maurya on Wed, 2023-02-01 02:05
Category: 
Scoring

I am running the Rosetta version - rosetta.source.release-334.tar.bz2 for designing two proteins but no values are generated for the total score. All the important files regarding this are attached. Please look at it and help me with this. 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Error with options -dunbrack_prob_buried_semi and -dunbrack_prob_nonburied_semi

Submitted by SamuelGong on Fri, 2023-01-27 06:20
Category: 
Scoring

Hi,

using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context

...................................

 

the flags and log file were attached.

Please help, thanks

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Grafting using antibody.mpi.linuxgccrelease , the modelled structure does not have constant region of the antibody.

Submitted by SubhaK on Thu, 2023-01-26 21:29
Category: 
Structure prediction

Hello all,
Using this command to graft from a specific template
antibody.mpi.linuxgccrelease -antibody:blastp /home/rosetta/ncbi-blast-2.13.0+/bin/blastp -fasta antibody.fasta -antibody:h1_template  pdb_id
The modelled structure does not have constant portion of the antibody.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages

Subscribe to RSS - Unsolved