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Ambiguous constraints are ignored in ab initio

Submitted by mschneid on Wed, 2014-06-18 04:33
Category: 
Structure prediction

Dear Rosetta Commons,

I recently wanted to use a set of ambiguous constraints in structure prediction and I prepared a file that looks like this:

AmbiguousConstraint
AtomPair CB 26 CB 38 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 28 CB 61 BOUNDED 1.5 8.0 1.5 NOE
AtomPair CB 26 CB 61 BOUNDED 1.5 8.0 1.5 NOE
END_AMBIGUOUS

Unfortunately, it seems that the ab initio application is ignoring the ambiguous constraints. No constraints are used in the prediction and also there is not constraint score term in the final score file.

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Rosetta 3 - General

can't find standard or standard.wts in weights folder (?)

Submitted by ss10t on Tue, 2014-06-17 00:15
Category: 
Scoring

Mac OS 10.7, 64 bit (i7 processor)
Python version 2.75 (version 3.4.1 also installed)

Hey, new to both PyRosetta, Python, and molecular modeling in general, but I found the PyRosetta User's Guide and have been working through it-until I ran into an issue with the scoring functions.

It seems that the software cannot find the standard or the standard.wts file in the weights folder which is supposed to be used for creating scoring functions. Specifically, when I try the following sequence of commands:

-In [23]: name='standard'

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PyRosetta - Build/Install

using Rosetta to compute pH dependent binding?

Submitted by JuliusSu on Sun, 2014-06-15 20:28
Category: 
Scoring

We are interested in creating a protein that will bind to a hormone at physiological pH, but unbind to the hormone at acidic pH, encountered when the complex is cycled through the cell. To do this, we would like to use the pH_mode functionality developed by Kilambi and Gray (Biophys Journal 103:587-595, 2012).

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Rosetta 3 - Applications

segfault in membrane_abinitio2.mpi

Submitted by siegert on Sat, 2014-06-14 15:56
Category: 
Compilation

I am getting a segmentation fault when running membrane_abinitio2.mpi with more than 2 processes. The segfault happens on line 161 in JobDistributors.cc when
job_recieved is false. Moving the statement into the preceding if block solves the problem. The patch is attached.

Cheers,
Martin

--
Martin Siegert
WestGrid/Computecanada
Simon Fraser University

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Rosetta 3 - General

no template pdb provided for alignment

Submitted by HZHANG020 on Sat, 2014-06-14 06:27
Category: 
Structure prediction

Dear rosetta user:
I have try to learn the tutorial in electron_density/cryo_em tutorial /scenario2_close_homology/, but when I run the run2_relax_cm_inputs.sh, there is no output, and only a warning messege, say "protocols.comparative_modeling.ThreadingJobInputter: Warning: no template pdb provided for alignment ". Can any one tell me how to solve this problem, thanks a lot. The content in run2_relax_cm_inputs.sh is show as follow, and I have a file 1OJ8A.pdb in the fold.

!/bin/bash

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Rosetta 3 - General

ddG_monomer

Submitted by cott1117 on Thu, 2014-06-12 09:53
Category: 
Structure prediction

I am trying to use ddG_monomer in Rosetta 3.5 to examine the structural effects of a single point mutation. Based on experimental data, it appears as if the mutation causes changes to the backbone of the structure. I would like to use the Monte Carlo ensemble method (protocol 20) from Kellogg et al. paper to model these changes but have not been able to locate the ensemble_generator_score12_sidechain_ver2.linuxgccrelease application listed in the supplementary methods section of the paper. Is the backrub application equivalent to ensemble_generator the application?

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Rosetta 3 - Applications

Enabling N-Linked Glycans

Submitted by jzabilansky on Thu, 2014-06-05 11:51
Category: 
PyRosetta

Hello,

I am currently trying to analyze a crystal structure that has various N-linked Glycans attached and would like to be able to work with these glycans in PyRosetta. However, if I try to work with the structure without cleaning it I receive the error message:

>>>pose = pose_from_pdb("my_molecule.pdb")
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 9172 residue types

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PyRosetta - Applications

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