You are here

Home

Scoring

running in MPI mode and multiple scores per output PDB file?

Submitted by dantimatter on Wed, 2019-10-30 09:42
Category: 
Design
Scoring

Hi Forum 
I recently did a Rosetta fixbb run with MPI and found that the score file had a lot more lines of output than there were actual PDB files. Specifically, I've got 353 scores in score.sc but only 12 PDB files.  is it possible that the parallel processors are simply overwriting the PDBs?   Is there a flag I should be including to avoid this? 

Thanks!  

Post Situation: 
Solved
Forums: 
Rosetta 3 - Applications

An error with score app

Submitted by Genta on Tue, 2019-10-29 18:46
Category: 
Scoring

Hello, I am trying the score app in the tutorials and meet an fatal error.

I work on CentOS 7 and my rosetta version is rosetta_src_2019.40.60963_bundle.

At first, I just used the command given by the instruction, it is:

score.mpi.linuxgccrelease -in:file:s input_files/1qys.pdb -in:file:native input_files/from_rcsb/1qys.pdb -ignore_waters

however, it stoped after a few seconds and the last lines of log is:

 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Alanine Scanning for 1 Protein (no interface)

Submitted by mags33 on Fri, 2019-10-25 10:08
Category: 
Design
Scoring
Enzyme Design

Hi, does anyone know how to do alanine scanning for just one protein?

I looked at different movers for RosettaScripts, like ddgScan, AlaScan, and ddg. Can any of these be used for a single protein with no interface? I want to see which protein residues are good targets for mutation.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

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 ] 

Post Situation: 
Unsolved
Forums: 
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 

Post Situation: 
Unsolved
Forums: 
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#)

 

Post Situation: 
Solved
Forums: 
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)

Post Situation: 
Unsolved
Forums: 
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?

Post Situation: 
Unsolved
Forums: 
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.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Applications

Pages

Subscribe to RSS - Scoring