You are here

Home

Unsolved

The problem hasn't been solved

How to specify constraints during fold-and-dock?

Submitted by sarah_b on Tue, 2020-05-12 01:55
Category: 
Structure prediction
Docking
Constraints
Symmetry

I'm folding a protein which is a trimeric long helix bundle.  I started from the main/demos/public/symmetry_examples/fold-and-dock/ and added my info (sequence, fragments etc).  This basically works but a lot of the resulting folds are globular not long - the helixes fold over on themselves.  I'd like to constrain this to extended conformations only.

I looked at constraints in the Rosetta docs, and tried creating input_files/constraints.cst to give a penalty to any structure which has less than 50-70 A distance between residues 1 and 63:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How to run partial_thread in RosettaCM when residure are more than 9999?

Submitted by lanselibai on Mon, 2020-05-11 22:43
Category: 
Structure prediction

One step in RosettaCM is 

partial_thread.default.linuxgccrelease -in:file:fasta JN254802.fasta -in:file:alignment JN254802_5tx1.grishin -in:file:template_pdb 5tx1_clean.pdb

But there are more than 9999 residues in the JN254802.fasta. The output "5tx1_clean.pdb.pdb" writes residue number 10000, 10001, 10002, etc as 1000, because only four positions are allowed for residue numbering (see the example in the end of this post).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Error with filter in rosseta_scripts

Submitted by Osmany Guirola on Mon, 2020-05-11 04:52
Category: 
Design

Hi 

i am working inthe design of peptides using the genkic mover. I am trying to implement a filter with "PeptideInternalHbondsFilter" to remove unwanted structures. When i run the rosetta_scripts  command this is the output.

From line 42:
Error: Element 'PeptideInternalHbondsFilter': This element is not expected.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

How to concatenate the 3-mer and 9-mer files for RosettaCM?

Submitted by lanselibai on Fri, 2020-05-08 05:38
Category: 
Fragment Generation

I am now working on a protein with multiple chains, and the total amino acids exceeds 1000. So I need to submit each chain one by one, get the individual 3-mer and 9-mer fragments, then concatenate them.

http://old.robetta.org/fragmentsubmit.jsp

The attachment is the 3-mer file. After concatenating them, do I only need to adjust these three places?

I will then use the 3-mer and 9-mer for the RosettaCM.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

General question regarding ligand-docking

Submitted by Alison_Yajie on Thu, 2020-05-07 09:48
Category: 
Docking

I am quite new to Rosetta. I have a very simple questions regarding general concepts about ligand-docking. I am a little bit confused about how to set parameter to ensure that all conformers generated can be tested. Lets say if I have a PDB containing 50 conformers. If I set -nstruct = 1 and run docking.xml with transformer like this (Transform name="predock" chain="X" box_size="20" move_distance="2" angle="20" cycles=“500” repeats=“2” temperature=“5”/>). What does really happen through the docking simulation? 

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Affinity optimization with GreedyOptMutationMover

Submitted by wentlewi on Thu, 2020-05-07 08:29
Category: 
Compilation

Hello

Can someone please give an example of a simple xml file and commandline for running the GreedyOptMutationMover to optimize the affinity of an interface of 2 proteins in a PDB file by mutation residues in a sequence of one of the proteins? The protein being mutated is relatively stable but the mutations are in a loop. What taskoperators and additional movers (repacking or backrub?) are necessary for doing this and reporting the change in ddG?

Thanks!

Post Situation: 
Unsolved
Forums: 
PyRosetta - General

Rna Denovo

Submitted by helderveras on Wed, 2020-05-06 08:40
Category: 
Nucleic Acids

Dear all,

Im using RNA Denovo rosetta protocol to build a 3D model of a small RNA segment (~10 nucleotides). For a specific purpose, i would like to model a ensemble of this ssRNA segment avoiding base pairing. I tried to modify some parameters but the ssRNA built is always packaged, with some base pairs. Is it possible to model such ssRNA using Rna Denovo protocol? 

 

Thanks in advance for any help!

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Template/Input length mismatch error during RosettaCM

Submitted by marinok on Mon, 2020-05-04 13:12
Category: 
Structure prediction

Hi,

I'm trying to generate homology models for metalloproteins.  I'm working with a test case right now to keep things as simple as possible, and  I'm getting this error which I cannot figure out:

protocols.hybridization.FoldTreeHybridize: [ ERROR ] Template 2 has a residue with PDB number 262 but the input protein only has 261 residues.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

I made a RDKit Chem.Mol to params converter — feedback welcome!

Submitted by matteoferla on Sun, 2020-05-03 10:14
Category: 
Small Molecules

For a project I was really in need of a clean way to convert a RDKit Chem.Mol object to a params file as the way I was making params files was horrid.

So I ended up writing a MIT-licenced python module that can load and save params files and do "surgery" on them or create one from a RDKit Mol object, which can include the dummy atom (*) which becomes a connect entry. It can be used without either rdkit installed (surgery only!) or pyrosetta installed (no testing method).

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pages