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Structure prediction

Failing Fragment libraries us Chemical shifts with Robettaa

Category: 
Structure prediction

Hi,

Robetta server is failing to generate fragment libraries with backbone chemical shift input for the past week!. my current job is at (http://www.robetta.org/fragmentqueue.jsp?id=39986). I also observed its failing for other users as well. can you please fix the issue.

thanks,
Kala

Post Situation: 

JobDistributor problem in antibody modeling

Category: 
Structure prediction

Hello everyone,

I build Rosetta 2015.12 on Scientific Linux 7 (SL-7). And, I follow the protocol of RosettaAntibody3 to do antibody modeling. 

(https://www.rosettacommons.org/docs/latest/antibody-protocol.html)

When, I run the script of “antibody.py” through following command as

Post Situation: 

Repeatability of DDG calculation

Category: 
Structure prediction

Dear all,
I have been trying to run a theoretical alanine scan on a protein.

Unfortunately, I cannot repeat the results I obtain when I run exactly the same experiment (just copy all files to a new directory and run again) more than one time. Attached is a png of the correlation between run 1 and 2. The black line is 1:1 correlation. You can see that some mutants look ok (green ring) while others are very badly different (red rings).

Post Situation: 

Total score problems with high-res ddg_monomer

Category: 
Structure prediction

Good Afternoon,

I'm running the high-res protocol of the ddg_monomer on a 439 residue enzyme structure (following the the Kellogg paper and online docs protocols) and I'm seeing some odd score outputs.

There are three types of odd outputs in the ddg_predictions.out file:

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Floppy tail: sidechain mutation during calculation

Category: 
Structure prediction

Hello

Recently, I am trying to predict flexible tail region of protein by using Floppy tail.

First I tried to use Floppy tail with test data (4tailstestdata.pdb).

I have run Floppy tail as below command

mpiexec -np 4 FloppyTail.mpi.linuxgccrelease -in:file:s 4tailstestdata.pdb -in:file:movemap mapmover -nstruct 4

//movemap
RESIDUE 90 117 BBCHI
RESIDUE 207 233 BBCHI
RESIDUE 324 351 BBCHI
RESIDUE 441 468 BBCHI

and I got 4 pdb files those file and each model has different amino acid sequence.

Post Situation: 

ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?

Category: 
Structure prediction

(relevant files can be downloaded at https://copy.com/yOhxRslZzK8j9z0l)

Dear friends,
In the instructions about ddg_monomer,

https://www.rosettacommons.org/docs/latest/ddg-monomer.html

it is mentioned that "the most accurate ddG is taken as the difference between the mean of the top-3-scoring wild type structures and the top-3-scoring point-mutant structures".

Post Situation: 

Access to latest CS-ROSETTA tools

Category: 
Compilation
Structure prediction
Fragment Generation

Have been trying to access the latest CS-ROSETTA tools without success for several days. Looks like www.csrosetta.org has been down for a while.

Any alternative to www.csrosetta.org to access latest cs-rosetta tools?

Post Situation: 

minirosetta: how to reserve (inter-chain) disulfides after relax ?

Category: 
Structure prediction

(I would appreciate it very much if any of my questions can be answered.)

Dear friends,
I have been trying to reserve the disulfides of my target protein during the minirosetta comparative modelling. However, though I have gone through many posts, I still could not work it out after using several disulfide related flags.

My situation is:

in the target protein:
Light chain (LC): residue 1-214
Heavy chain (HC): residue 215-442

Post Situation: 

force field, energy function

Category: 
Structure prediction

Hello everybody,

I am interest in, which force field Rosetta use and which energy functions are applied for a normal abinitio calculation. If I used an abinitio calculation with a metallatom, are there used a other force field for the zinc atom?!
Can anybody advice my a good paper which an easy explanation or something like that?!

many regards

Post Situation: 

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