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Structure prediction

missing residues while Rosie Modeling

Submitted by jguan on Mon, 2014-08-11 06:56
Category: 
Structure prediction

Hi all,
I submitted one job for anitbody variable domain structure prediction through Rosie recently. Rosie generated the pdb files. However, when I checked it through Chimera, we found the light chian C-terminal lost two residues (-RA). I double checked my submiting sequence, it was fine. Does anybody meet the similar issue? How could that happen and how to deal with it?
Thanks,
Jian

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ROSIE - General

Evaluating energies on non-standard rotamer set

Submitted by pachecoj on Sat, 2014-07-26 16:27
Category: 
Structure prediction

Without getting too detailed I would like to be able to compute all one-body and two-body energies for a set of chi angles that I have chosen (e.g. that are not from a rotamer library). I am evaluating for a set of angles for each chi rather than a single joint configuration, and would like to compute and store this set of energies. It seems like the way to go would be to build up a RotamerSets object on-the-fly as in:

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Rosetta 3 - General

relax job failed

Submitted by albumns on Sat, 2014-07-26 00:21
Category: 
Structure prediction

Hello:

I am trying to relax my protein with following parameters, but it failed with messages:

-database /home/albert/install/rosetta_2014/main/database
-nstruct $nstruct
-in:file:s $pwd/input.pdb
-relax:quick
-out:path:pdb .
-out:suffix $i
-out:file:fullatom
-out:pdb

core.pack.task: Packer task: initialize from command line()
protocols.jd2.JobDistributor:

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Rosetta 3 - Applications

Antibody protocol: unusual antibodies, and chainbreaks

Submitted by Cyril Cros on Mon, 2014-07-21 17:03
Category: 
Structure prediction
Loop Modeling
ROSIE

Hello,
I am doing a research internship, on modelling some antibodies recognizing a short peptide from a conserved part of the gp41 protein of the HIV1 virus and simulating their docking.

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Rosetta 3 - Applications

Question about wrong homology design

Submitted by mony2182 on Fri, 2014-07-04 10:26
Category: 
Structure prediction

Hi everyone, I have been using rosetta 3.4 and 3.5 to build an homology model of a protein and the result is the same, the structure is broken just in one of the amino acids. I made a control test and made the homologue model of the same template and also the structure is broken. In figure A is the template an in figure B is the homologue model where appears the some fragments of one residue outside of the structure, How can I solve that?
there is my script:

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Rosetta 3 - General

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

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

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