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Structure prediction

Atom_.cc line 304

Category: 
Structure prediction

Hi list,
I'm running the minirosetta.mpi threading protocol and everything seems to be working fine.
The query silent is been regularly updated and I can extra pdbs from it.
However, from time to time get the following error message on screen.

ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 304

Any ideas?
Best.
Fred

Post Situation: 

Missing residue coordinates in PDB files

Category: 
Structure prediction

Dear Sir or Madam,
I got a PDB file, in which some of the residue coordinates are not resolved (shown below, missing from 136-139). But I can still know the amino acid sequence. Can I ask what is the best way to estimate those missing coordinates?

I am thinking manually copy the coordinates of same type of residue to the PDB file, followed by minimization to some extent. Is this okay? What particular minimization protocol/restrain should I use?

Thank you very much.

Yours sincerely
Cheng

Post Situation: 

Adding 'virtual' residues for N- and C-terminal optimisation

Category: 
Structure prediction

Dear All,

I would like to optimise the N- and C-termini of a model, and would like to use some of the loop modeling protocols to do so. I have read in the documentation that virtual residues are required for this. How do you add these? Are there examples in the tutorials?

Post Situation: 

missing residues while Rosie Modeling

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

Post Situation: 

Evaluating energies on non-standard rotamer set

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:

Post Situation: 

relax job failed

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:

Post Situation: 

Antibody protocol: unusual antibodies, and chainbreaks

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.

Post Situation: 

Question about wrong homology design

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:

Post Situation: 

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