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Loop Modeling

Symmetry mode in Remodel for N-terminal extension

Category: 
Design
Loop Modeling
Symmetry

Hello, 

I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error: 

File: src/protocols/loops/loops_main.cc:253
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.

Post Situation: 

denovo modelling on a virus-coat protein dimer

Category: 
Loop Modeling

I am new to denovo modelling so your help will be greatly appreciated. 

 

I have a density map for a coat protein dimer of a virus (no previous structure of same or similar virus is known so homology is not an option). The two chains seem to swap domain so i cannot segment the dimer further. Rosetta seems incapable to handling a dimer for denovo modelling (each chain is 410 AA long) so i used phenix.map_to_model to get a partial map. 

Post Situation: 

Fragment Insertion to Generate a Loop

Category: 
Loop Modeling

Hello master builders/users,

I have a problem that I am encountering in my script that I (desperately) need some assistance with.   I am trying to generate Loops for a protein 4115 via fragment insertion method. I have attached my script for reference.

Here is what  am tryiing to acheive: 

Post Situation: 

antibody modeling error

Category: 
Loop Modeling

Hi all:

      I am going to use antibody.default.linuxgccrelease to make a model for an antibody sequence.  The command I entered is ”antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database  /home/mxp/apps/rosetta/tools/antibody >error1.log“.  I encountered the following error:

.......

core.conformation.Conformation: current variant for 207 CYD
core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner
caught exception 

Post Situation: 

Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking

Category: 
Loop Modeling

Dear Sir or Madam,

I got a one complicated problem, which took place during loop modelling for protein-protein docking. I carry out tasks from the Meiler tutorial for Rosetta.

Post Situation: 

input file for loop modeling

Category: 
Loop Modeling

Hello

I want to repair my missing residues by loop modeling. As it has shown In the demos and tutorial, I should have a file like x_missing_loop.pdb

it is like main pdb file of target protein BUT it hase something called table energy pose bellow it. How I should make this table energy pose. ???? tutorial has not said anything about making this table energy pose

I have attached that input file from demos, please explain how I can make table pose energy which is under cordinations data?

Post Situation: 

perturb_temp flag

Category: 
Loop Modeling

Dear all,

I am trying to understand this flag better. I believe the default temperature for Monte Carlo is 0.8 but I cant find out what does that actually mean during the Monte Carlo steps. I thought the temperature varies during those steps.

Can someone either explain this to me and point me to a easy to understand paper?

 

Thank you!

L.

Post Situation: 

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