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- OS type,
- OS version
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for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

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Thank you!

Post Situation: 

Predicting the part of protein strcutrue

Category: 
Structure prediction

Hi,

I have a protein whose sequence is fully known and whose structure is partial known. Most sequences of the protein are folded in the luminal ER domain and this part is resolved by experiments. However, transmembrane and cytosolic parts of the same protein are not resolved. As only the luminal part of the protein is resolved, I would like to predict the structure for transmembrane and cytosolic domains. Is there a way to predict only these parts while I keep the experimentally-resolved luminal domain?

Thanks, Siyoung

Post Situation: 

DockingProtocol mover ensemble error

Category: 
Docking

Hi all,

I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.

I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.

If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:

 

...

Post Situation: 

Error in enzyme_design.default.linuxgccrelease: corrupted size vs. prev_size

Category: 
Design
Enzyme Design

Dear Rosetta Team,

I am trying to run enzyme design protocol on protein model with 2 Iron ions, 2 Ions, 1 molecule and 1 water molecule (!). Problem is it is getting core dump/segmentation fault each time I run it. After various code recompilations and printing the error I came came to know the error is at "EnzdesBaseProtocol::enzdes_pack(" in EnzdesBaseProtocol.cc.

code:

Post Situation: 

cartesian_ddg output

Category: 
Design

I am following the protocol

https://www.rosettacommons.org/docs/latest/cartesian-ddG

to predict the ddG of a monomer after a point mutation. I am using Rosetta 3.10.

The output file, mutfile.ddg, looks like this:

COMPLEX:  Round1: WT ...

COMPLEX:  Round2: WT ...

COMPLEX:  Round1: MUT_1ALA ...

etc.

Instead of COMPLEX, I was expecting to see lines beginning with

BEFORE_JUMP: RoundX:

Post Situation: 

Warnings during relax

Category: 
Design

I am getting  a lot of warnings like this:

core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 53 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 92 BRANCH 1
core.optimization.Minimizer: [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!
 

This is using the following relax command:

Post Situation: 

Negative Design

Category: 
Docking

Hello,

 

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

Post Situation: 

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