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Structure prediction

Predicting conformations of mutated residues

Submitted by Delfosse57 on Tue, 2023-08-22 12:26
Category: 
Structure prediction

Hi all,

I am attempting to predict the conformations of an enzyme after a single mutation. I have been using pymol to place the mutation into the protein and then I use the rosetta relax application to optimize the structure. Is this a valid way of performing this technique? Or should I be using rosetta scripts and repack the sidechains instead. I am worried that the relax protocol may not be able to optimize the residue if pymol puts it in a conformation that is far away from the optimal conformation.

Thank you!

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Rosetta 3 - General

ValueError("Path %s does not exist!" % path_name) for rna_helix.py

Submitted by kameisel on Wed, 2023-08-16 00:39
Category: 
Structure prediction
Nucleic Acids

Hi everyone,

I want to model helices with rna_helix.py but I get an error that rna_helix.linuxgccrelease isn't in the path where python script is looking for it:

File "/home/software/rosetta_bin_linux_2021.16.61629_bundle/main/tools/rna_tools/bin/rna_helix.py", line 27, in <module>

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Rosetta 3 - Applications

Antibody Structure Prediction - Error on antibody_H3 step: "Option matching -antibody:remodel not found in command line"

Submitted by ramon-arg on Mon, 2023-07-24 17:56
Category: 
Structure prediction

I'm trying to predict the structure of an antibody by following this Rosetta Antibody Modelling tutorial: https://meilerlab.org/wp-content/uploads/2022/02/RosettaAntibody_tutorial.pdf

At the 5th step, during the refinement of the model, I find the following error:

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Rosetta 3 - Applications

rosetta_cm - ERROR: Assertion `tlen < slen` failed on File: src/core/fragment/util.cc:177

Submitted by ramon-arg on Thu, 2023-07-13 18:41
Category: 
Structure prediction

I'm following this tutorial to run a protein structure prediction: https://new.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

I was able to model one protein sequence successfully following those steps, but trying for different ones I've been getting this same error:

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Rosetta 3 - Applications

fragment_picker:[ ERROR ] UtilityExitException ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz

Submitted by yueyuedake on Wed, 2023-07-12 03:36
Category: 
Structure prediction

Hi,

When I run fragment_picker, it gives the message:

ERROR: can't open file: $ROSETTA/tools/fragment_tools/vall.jul19.2011.gz
ERROR:: Exit from: src/protocols/frag_picker/VallProvider.cc line: 17
 

the detail message as follows:

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Rosetta 3 - Applications

Scoring correlation with electron density map

Submitted by mrosam on Thu, 2023-05-25 05:14
Category: 
Structure prediction

I am trying to score how well different protein models fit into one electron desity map. I have tried using the score_jd2 tool with the flags:

"-database /programs/PDB/rosetta-3.13/main/database -in:file:s ./structures/*.pdb  -edensity:mapfile ./emd_12705.map -edensity:mapreso 3.6 -edensity::realign min -cryoem_scatterers true -grid_spacing 2.0 -fastdens_wt 35.0"

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Rosetta 3 - General

Simple_cycpep_predict with crosslinker BBMB

Submitted by Ken on Tue, 2023-05-09 08:52
Category: 
Structure prediction

Hi all,

I'm trying to use simple_cycpep_predict with crosslinker BBMB, and the generated structure (see attached) does crosslink with BBMB.  However, it also does a head-to-tail cyclization between the 2 termini and I would like to not have that happen.  It's not clear to me from the help file how to do that as the default uses head-to-tail cyclization.  Is there a way to turn that off?

Here is the sequence file, the parameters that I'm using, as well as one of the generated structures to illustrate what I am having issues with.

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Rosetta 3 - Applications

Your compiler does not have full support for C++ll regex, and therefore can't suport RegEx_based_CDR_Detector/antitody grafting.

Submitted by ldx022 on Thu, 2023-03-09 17:03
Category: 
Structure prediction

Hi there,

One problem with the initial use of antibody application is that there is complie issue shown as the following:

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