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Scoring

ΔG Calculation with PyRosetta

Category: 
Scoring

I have been reading some post looking for an anwer to my question but I still not complitely sure about it. I understand that for a complex, what rosetta gives you is a score that it is no exacly the DG. I would like to know if with the next code, using the standard score funcion, I can calculate for a comple of 2 chain the DG with the formula:

DG= Score_complexe - (Score_chain_A + score_chain_B)

Post Situation: 

How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?

Category: 
Scoring

Hi, I am doing the design of a batch of decoys.

I want to block the designs of residues 1-9 and residues 80-91 for all the pdbs.

However, some of the pdbs do not have certain residue numbers (e.g. pdb1 has missing residue number 1, pdb2 has missing residue number 82).

May I know how to specify residue numbers so I can still use a single resfile for the whole batch of pdbs?

Post Situation: 

Choosing weight file for interface design?

Category: 
Scoring

Hi, I am now trying to do an interface design of a nanobody docked to the target (through its CDRs, by patchdock).

I have some doubt about choosing the best weight file for scoring of the designs. May I have some suggestions from you?

Actually, I have read from here and I have already learned that:
1) Choose score weighting by finding what was used for the most similar application in published literatures.

Post Situation: 

Memory leak when PDB preparation

Category: 
Scoring

Hi everyone,

   I am preparing the pdbs from pdb.org for scaffold. About more than 6000 pdbs were downloaded and have been preparing. However, the memory leak was encountered. I have try to use -linmem_ig 10 and -jd2:delete_old_poses to resolve the problem. But the memory leak is still there. 

Could you help me to solve this problem?

   Thanks a lot.

Post Situation: 

Error with etable_atom_pair_energies()

Category: 
Scoring

I am new to Pyrosetta and programing and I am learning how to use Pyrosetta. So when I was practicing scoring with Workshop #3 bullet point 5, I came across a error, and I have no idea what's wrong with.

Here is what I did. 

r1 = pose.residue(24)

r2 = pose.residue(20)

a1 = r1.atom("N")

a2 = r1.atom("O")

etable_atom_pair_energies(a1, a2, scorefxn)

Post Situation: 

ddG calculations to study point mutations

Category: 
Scoring

Hi,

I am using Rosetta protocol to determine ddG changes on point mutations in a peptide bound to a protein complex. I first used FastRelax to remove any steric clashes in the protein structure and then ran the ddG protocol to generate ~1000 structures till there is no change in ddG values. I now want to build a correlation plot between the Rosetta ddG values and experimental calculations.

Post Situation: 

InterfaceAnalyzer packstat score = 0.000

Category: 
Scoring

Hello

I am using the InterfaceAnalyzer to obtain packing scores of antibody-antigen strucutres from the PDB database but the packstat score always ends up being 0 for some reason. I am specifying for the activation of packstat calculation as can be seen in my flags.txt file below

-in:file:s 1A14_atomlines.pdb
-interface HL_N
-compute_packstat = 1
-out:file:score_only 1a14_interface.out

The output file is attached below. 

Post Situation: 

Rosetta lack of necessary application

Category: 
Scoring

Hi

    when i learn denovo_model_building from demos/public/electron_density_structure_refinement.In step 1 and step2 ,they ask for place_fragment_into_density.linuxgccrelease,  cal_overlap_score.static.linuxgccrelease,cal_nonoverlap_score.static.linuxgccrelease.In my rosetta 3.0 i can not find these application.I dont know why,thanks for help

Post Situation: 

Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

Post Situation: 

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