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[dev] Using h-bonding values in new energy term

Category: 
Scoring

Hi all,

I'm implementing a new energy term and need to weight it based on the bb h-bonding energy of this residue and the two residues it is bonded to. It is a ContextDependentOneBodyEnergy and I have everything working except this weight. Obviously rosetta already has methods that calculate hbond_lr_bb and hbond_sr_bb. My question is - what is the best way to get the hbond energys of the residues in my energy method?

Thanks!

-Igor

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Interface Analyzer Segmentation Fault

Category: 
Scoring

Hello,

I relaxed the homodimeric biological assembly of PDB 1ISA, and am trying to use Interface Analyzer to calculate the interfacial energy between the subunits. I have cleaned the strucutre to removed all the water, metals, et.c and leave only the protein residues. Below are the command line flags I am using:

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Different weights in the constraints for each stage of AbinitioRelax

Category: 
Scoring

As each stage of AbInitio protocol call a different function (score0, score1, score2, score5 e score3), it appears to me that use a single cst_weight in my command line doesn't make sense (a single weight for every single stage). For that reason, I would like to test different weights for cst in each stage of Abinitio.

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Altering substrate specificity

Category: 
Design
Scoring
Enzyme Design
Small Molecules
Chemically Modified Residues

Hi all,

I'm presently working on a project to modify the substrate specificity of a DNA polymerase for non-natural nucleic acids.

I've currently been using the GreedyOptMutationMover with a ddg filter (jump across the substrate) for a 10Å shell around the active site and identified several single point mutations that have been experimentally validated to improve activity.

However, one of the problems with greedyopt is that it does not appear to screen every possible position or single point mutation within the designable region.

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dG_separated threshold for identifying non-binding peptides with InterfaceAnalyzer.

Category: 
Docking
Scoring

Hello,

I am a beginner in protein modelling/analysis and trying to learn through tutorials and the forums here.

A bit of a background of my present Task: I have a crystal structure of an Ab-Ag complex (AbFab with Ag peptide). I also have experimental data on binding affinities of several Ag peptide variants. I want to use this data to predict binding ability of novel Ag peptide variants with the same Ab.

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How to transform a pose from symmetric into non-symmetric?

Category: 
Design
Scoring
Constraints
Symmetry

Hello,

Is there a way to break the symmtery of a pose in the middle of a Rosetta script? I want to avoid writing the PDBs and feeding them again to a new script.

Any suggestion is highly appreciated!

Thanks!

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DomainAssembly Mover with constraints (using RosettaScripts)

Category: 
Docking
Scoring
Constraints

Hello,

I am trying to run the domain assembly protocol while atom_pair constraints . I am using RosettaScripts for my application.

I have tried including the constraint file in the xml script using the ConstraintSetMover and Reweighting the score function. I have also tried included the constraint file in the flag file using -constraint:cst_fname. Yet the output silent do not seem to include the atom_constraints score term.

I would appreciate any help on how to include the constraints in the scoring function for domain assembly.

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RMSD calculation

Category: 
Scoring

Dear all,

Hi,

I need help with Ca-RMSD calculation. I've used docking protocol to generate some models and now I want to calculate Ca-RMSD between these models and the native. Each model has 5 chains: e.g. model_AB_CDE. I want to calculate Ca-RMSD in a way that the model_AB chains would be aligned on native_AB and the RMSD between model_CDE and Native CDE will be computed. How can I do that? I've used score protocol but it computes the total RMSD between all the chains.

Thanks in advance,

Best,

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BridgeChainsMover

Category: 
Design
Scoring
Loop Modeling

Hi,

I am using the 2016.28 build and have the some problems with "BridgeChainsMover" from Brian's recent method paper: DOI:10.1007/978-1-4939-3569-7_20

I get this error "ERROR: 'scorefxn' is not a valid option for BridgeChainsMover".  Here is the part of script that returns an error:

<BridgeChainsMover name="connect" chain1="1" chain2="2" motif="3LX-3LA-3LX" overlap="3" scorefxn="centroid_scorefunction" />

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