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mutate_residue doesn't mutate

Submitted by dsim on Wed, 2015-03-18 02:32
Category: 
Design

Hello,

In my version of PyRosetta, which I downloaded in december 2014, the mutate_residue function doesn't mutate the sequence of the Pose...

Here is the relevant part of my code:

for j in sequence:
(...)
mutate_residue(pose,resn,j, pack_scorefxn=score_fxn)
(...)
jd.output_decoy(pose)

When I do this, pose doesn't change even though its whole sequence should be replaced.

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PyRosetta - General

References where Rosetta is used to compute ddG of binding after mutation?

Submitted by cossio on Tue, 2015-03-17 05:13
Category: 
Design

Rosetta has some applications that can be used to setup a protocol to compute the ddG of binding upon mutation (relax, fixbb or ddg_monomer to create wt structure and mutated structure, InterfaceAnalyzer to compute binding energies, etc.) Are there references available where Rosetta is used this way? Until now I have found papers where the authors either fit their own energy function to experimental data (instead of using Rosetta's energy function), or they use other applications (molecular dynamics, for example) to relax their structures, or something else.

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Rosetta 3 - Applications

Building 3.4 on Debian Linux 7.8 (wheezy) using g++ 4.7.2

Submitted by hansellt on Mon, 2015-03-16 10:34
Category: 
Compilation

I get the following error that terminals the build process:

src/protocols/jd2/SingleFileBuffer.cc:148:13: error: 'sleep' was not declared in this scope

It would appear that for this system "sleep" is found in the <unistd.h> include file.

Anybody else had this problem ?

Or is this a "dead" issue since 3.4 will not be getting any more updates ?

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Rosetta 3 - Build/Install

​​B​3​-protein design using rosettaScript movers

Submitted by straore on Mon, 2015-03-16 05:05
Category: 
Non-Canonical Peptides

​
Hello everyone,
I am tryi​ng to perform a ​​B​3​protein​ design tests ​using ​rosettascript (rosetta demo model). I have 3 ​designable ​positions ​and I am interested in the functionalit​ies​ of ​the movers:​"RandomMutation" and "GreedyO​ptMutationMover​"

Using these movers, none of my design positions have been taken into account as a designable! In the log file, there are warnings
indicating that there is no design position.

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Rosetta 3 - General

Total score problems with high-res ddg_monomer

Submitted by jklesmith on Tue, 2015-03-10 15:54
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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Rosetta 3 - Applications

Floppy tail: sidechain mutation during calculation

Submitted by syoifczeri on Mon, 2015-03-09 19:01
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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Rosetta 3 - Applications

Conformers in EnzDes

Submitted by JorickF on Fri, 2015-03-06 04:41
Category: 
Enzyme Design

Hello,

I have two questions concerning conformers in the enzyme design application:

1) Is hydrogen bonding calculated from heavy atoms only or should the conformer library contain, for example, hydroxyl groups with the hydrogen pointed in multiple directions for it to recognize when a hydrogen bond can be formed?

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Rosetta 3 - Applications

the ddg of mutant is same as the wt

Submitted by deepanshuiitb on Wed, 2015-03-04 11:56
Category: 
Design

Hi,
I am trying to find the ddg for my mutant protein-protein complex using the resetta script in calculate_protein_protein_ddg application. I have done it with -ntruct 5 and all of them gave the same values. But I am getting the same value for both the mutant and the WT.I am not sure what's wrong.Can anyone suggest something if they have an idea?

Thanks!

I am uploading my PDB and the score file. Chain A and B represent the 2 protein in the heterodimer respectively.It also has heteroatoms at the end.

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Rosetta 3 - Applications

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