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Structure prediction

Relaxed proteins show higher clash score in molprobity results.

Submitted by Wang Zhe on Fri, 2021-12-03 04:32
Category: 
Structure prediction

Hi everyone,

I am tring to refine the predicted structure from alphafold and SWISS-MODEL database. Since the protocol I followed said I need to eliminate the steric clash and do refinement in predicted structure first (and then docking or some other analysis).

So I just relaxed protein in torsion space with constraints. And here is the code I used:

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Rosetta 3 - Applications

pyrosetta.rosetta.core.pose.rna

Submitted by chenjief on Tue, 2021-11-23 07:03
Category: 
Structure prediction

hey,

Enclosed the final model and problem. I use the pyrosetta.rosetta.core.pose.rna to build RNA 3D strucutre. When I check the final results, I found that 

the base part is not connected to backbone.  I want to know how to solve this problem.

Best wishes,

Chenjie

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Rosetta 3 - General

Problems with waters in CoupledMoves application

Submitted by Corvin on Tue, 2021-11-16 07:16
Category: 
Structure prediction
Docking
Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

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Rosetta 3 - Applications

farfar2 error

Submitted by debostuti on Thu, 2021-10-07 23:10
Category: 
Structure prediction

Hello

I am trying to model a 514-nt long RNA structure using farfar2. My job failed with the following error

ERROR: Not complementary at positions A    8 and U   13

I do not understand this, A and U are complementary  and I have checked both the input sequence and dot bracket files and I dont see any discrepancies. Attaching both inputs and the Rosie crash log file. Could someone please help me sort the error.

Thank you

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ROSIE - General

antibody - sequence position requested was 0

Submitted by jremmel on Mon, 2021-09-27 12:26
Category: 
Structure prediction

Hi,

I am trying to do some antibody structure prediction. During the grafting step for the sequence I am working with, it seems to get through making 4 models, but then crashes with the error message: 

[FILE]: src/core/conformation/Conformation.hh

[LINE]: 509

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

Anyone have any idea what is going wrong here? 

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Rosetta 3 - Applications

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Submitted by rlwoltz on Tue, 2021-08-03 23:26
Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

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Rosetta 3 - General

rosetta_cm segfault

Submitted by browns02 on Fri, 2021-07-09 13:35
Category: 
Structure prediction

I set up a homology model with the setup_RosettaCM.py
It creates a set of threaded models, an xml file with commands, and a flags command that points to the input file and the xml. When I run the rosetta_scripts command with this flags and xml, I get a segmentation fault. I find the error messages difficult to understand. 

Here is the command, screen output, flags, xml, and CRASH.log

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