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Structure prediction

Chi values for side chains when switching from centroid mode

Category: 
Structure prediction

Hi all,

I was wondering how Rosetta handles (full atom) chi values when switching from centroid mode to full atom? Does it use some average value? Does it read in the bb angle and look up the dunbrack rotamer value(s)? Or something else?

Thanks

Mark

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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

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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

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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).

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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.

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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".

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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?

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