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InterfaceAnalyzer：“too many tries in fill_missing_atoms!”

Submitted by mxp on Tue, 2019-08-06 00:41
Category: 
Scoring

Hey Guys,

We are trying to use  "InterfaceAnalyzer"  to  analyze a  PDB,  then we get this:

......

.....

core.conformation.Conformation: [ WARNING ] missing heavyatom: C7 on residue pdb_HSD 152
core.conformation.Conformation: [ WARNING ] missing heavyatom: O4 on residue pdb_HSD 152
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'complex_0_0001'
Error: [ ERROR ] 

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Rosetta 3 - Applications

Question about fastsaxs and saxs_score

Submitted by orionshih on Thu, 2019-06-13 02:30
Category: 
Scoring

Hi,

I am trying to incorporate saxs score to my calculation, from some digging into this forum I got that fast_saxs term calculate the SAXS scattering curve from fullatom protein model and saxs_score term would calculate the curve from centroid-based model. My question is, can it work on heavy atom and nucleic acids? Thanks in advance...any comments or suggestions would be appreciated!

Orion 

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Rosetta 3 - Applications

individual residue score

Submitted by yijietseng on Wed, 2019-05-29 09:59
Category: 
Scoring

Hi all,

I just have a question about the individual AA score. So I am trying to compare the total score (with proper weighted scoreterms) and the individual AA score. 

For the total score I used:

scorefxn = get_fa_scorefxn()

score = scorefxn(pose)

To get the weighted indicidual AA score I used:

pose.energies().residue_total_energy(residue#)

 

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PyRosetta - General

ΔG Calculation with PyRosetta

Submitted by Sandra on Tue, 2019-05-21 00:26
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)

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PyRosetta - General

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

Submitted by johnnytam100 on Wed, 2019-05-08 02:30
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?

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Rosetta 3 - General

Choosing weight file for interface design?

Submitted by johnnytam100 on Tue, 2019-05-07 00:47
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.

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Rosetta 3 - Applications

Memory leak when PDB preparation

Submitted by Jacky010 on Mon, 2019-05-06 01:28
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.

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Rosetta 3 - General

Error with etable_atom_pair_energies()

Submitted by yijietseng on Mon, 2019-01-28 14:00
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)

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PyRosetta - General

ddG calculations to study point mutations

Submitted by N.Chopra on Fri, 2018-12-07 12:36
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.

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Rosetta 3 - Applications

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