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Homology modelling applies alignment wrong

Submitted by bernhardcl on Thu, 2015-08-06 09:39
Category: 
Structure prediction

Dear all,

I have been battling with a specific homology modelling for some time (I never had problems before though) and hope that you can help me further. Whichever version of homology modelling I use (3.5 and never hybrid one from the latest release), the sequence of the final model does not correspond to the sequence of the alignment I provid. It appears that a gap very early in the alignment is skipped and all following residues are hence shifted by 2 (only one more gap in ~450 res). For simplicity just the first few residues:

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Rosetta 3 - Applications

score:weights for fixbb application in Rosetta 3.5

Submitted by tylerborrman on Tue, 2015-07-28 14:16
Category: 
Design

Hi,

If you specify a weights file using the option '-score:weights' , will that weighted scoring function be used in optimizing side chain placement? That is, does the simulated annealing algorithm incorporate the scoring function specified by '-score:weights', or is 'score:weights' only used in the final scoring of the structure AFTER side chains are placed and the designed PDB is complete?

Thanks,
Tyler

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Rosetta 3 - Applications

Homology Modelling with cofactors

Submitted by Derek Smith on Thu, 2015-07-09 08:24
Category: 
Structure prediction

Hi guys,

Can the RosettaCM protocol include cofactors as residues/restraints in model building?

I am building a cytochrome P450 model and I'd like to include the haem if possible. Without the haem, some of the cofactor-interacting backbone has subtle conformational differences.

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Rosetta 3 - Applications

Chi values for side chains when switching from centroid mode

Submitted by MarkW on Fri, 2015-07-03 04:43
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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Rosetta 3 - General

rotamer library in coupled_moves

Submitted by mtyras on Fri, 2015-05-29 07:46
Category: 
Docking
Enzyme Design
Small Molecules

Hello, 

 

Recently, I had a chance to see a presentation about coupled_moves. There is hardly any information about it since the paper isn't published yet but I figured I would give it a try anyway. What I want to do is to redesign enzyme specificity for a new substrate . The problem is including rotamers library of my new substrate. 

 

I created ligand rotamers with Frog2 (no acces to MOE or OpenEye) and created params files with:

 

"molfile_2_params.py rotamers.mol2 --conformers-in-one-file".

 

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Rosetta 3 - Applications

Failing Fragment libraries us Chemical shifts with Robettaa

Submitted by kalabharath on Tue, 2015-04-28 19:33
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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Rosetta 3 - Applications

Compiling cxx=icc; "icc: command not found"

Submitted by novosirj on Thu, 2015-04-02 08:50
Category: 
Compilation

I'm having what I imagine to be a simple to solve problem where I'm just missing something. I am running on RHEL5 and trying to build Rosetta 3.5. I have the Intel Composer compiler v15.0.2. I know that no newer than about 11 is shipped in the config options, but I've successfully updated the file before to go so far as 14.0.1. In any case, this appears to be failing well before that would matter. The following occurs when I try to build:

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Rosetta 3 - Build/Install

"No Python class registered..." when trying to access SymDofs

Submitted by pitmand on Tue, 2015-03-17 14:29
Category: 
Symmetry

I can create symmetric systems without any issue in PyRosetta, but I can't access the symmetric dofs at any stage. It produces a message like this:

In [84]: dofs = symm_info.get_dofs()
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-84-f37670432e61> in <module>()
----> 1 dofs = symm_info.get_dofs()

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PyRosetta - General

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