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[dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation

Submitted by ipetrik_ambry on Thu, 2018-01-18 12:26
Category: 
Loop Modeling

Hi,

I'm trying to determine the bond lengths between consecutive residues in a Pose/Conformation, to determine whether they are actually close enough to be bonded, or if there is a gap between the residues that needs to be closed or filled in. Is there a straightforward way to do this?

Thanks

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Rosetta 3 - General

Structure refinement with RDC constraint

Submitted by shushunur on Thu, 2018-01-18 00:44
Category: 
Structure prediction
Constraints

Hi~

I've done a structure refinement of a protein by Rosetta3.8.

However, I'm not sure that what I've done is correct or not.

The protocol that I followed are list below:

First, I put my protein sequence(.fasta file), torsion angle(predicted by talos+), RDC value(experimental data) into the website( http://robetta.bakerlab.org/fragmentsubmit.jsp) to do fragment generation.

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Rosetta 3 - General

Expanding the silent file

Submitted by jharamesh on Fri, 2018-01-12 09:15
Category: 
Structure prediction

Hi Rosetta Community,

With comparative modeling application I created a silent file output using following flags

-out:file:silent threaded_model.out
-out:file:silent_struct_type binary

Later, when I used the generated silent file as an input for other applications like "cluster" or "score", it crashed with an error.

ERROR: Assertion `is_int( tag )` failed.
ERROR:: Exit from: src/core/io/silent/RNA_SilentStruct.cc line: 292

 

Is there any easy fix for that?

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Rosetta 3 - General

Only Link to executables in bin

Submitted by Siaseb on Tue, 2018-01-09 08:36
Category: 
Compilation

Hi

Im new to Ubuntu and Rosetta. Installed Rosetta as per the guildelines and released bin by

./scons.py -j2 mode=release

But the bin only contains link to executables and hence when I try to run the De novo structure prediction tutorials, getting error message,

AbinitioRelax.default.linuxgccrelease: No such file or directory

can you please help.

Many thanks

Siaseb
 

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Rosetta 3 - Build/Install

changing the chain id

Submitted by aneamtu on Tue, 2018-01-09 00:08
Category: 
Structure prediction

Hi!

 

I need to change the chain ids for 10000 pdb structures generated by the relax protocol. I have 2 chains A and B in each protein (antibody) and I want to change them yo H and L (as antibody_H3 seems to request that the heavy chain of the antibody should be name d'H').  I saw in older posts that there should be an utility:

changeChain.pl - change the chain ID of a specified chain from a pdb file.

but I cannot find it the Rosetta source.

Any suggestions?

Many thanks,

Andrei

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Rosetta 3 - General

Can I thread a two chained structure in RosettaCM?

Submitted by ahmadkhalifa on Mon, 2018-01-08 09:41
Category: 
Structure prediction

Most Rosetta CM tutorials show a one chain example for threading. If my structure has two chains, is it possible to align and thread my two chained sequence and template in a one run.

What should the grishin alignment format for the two chains look like?

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Rosetta 3 - General

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