You are here

Loop Modeling

loop modelling on complex structure

Category: 
Loop Modeling

Hi,

I'm using next-generation kIC to model one loop , which interacts with another subunit in the hetero-trimer complex.

I'd like to input the whole 3-chain structure for loop modelling as adjacent subunit could stabilize the loop conformation because of the interaction.

But I've got no idea where I can designate the chain for loop modelling if I input multi-chain structure?

Could anyone please give me some ideas?

Thanks a lot,

Tianyang

Post Situation: 

Does antibody_numbering_converter support camelid antibody?

Category: 
Loop Modeling

Hi all,

      We downloaded Complex of a camelid single-domain vhh antibody 2P43, used Discovery Studio to change  the numbering scheme of the PDB file to  Chothia, then when we want to used "antibody_numbering_converter" to  change the numbering scheme of the PDB file from Chothia to AHo, an error occurred,  the command we used is " antibody_numbering_converter.linuxgccrelease -s 2P43_clo.pdb -camelid true -input_ab_scheme Chothia -output_ab_scheme AHo ",  the error is as follow:

Post Situation: 

Building loop extensions in a membrane protein with Remodel

Category: 
Design
Scoring
Loop Modeling
Membrane

Hi All,

I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.

Here are the flags that I'm using:

Post Situation: 

LoopModeler mover unable to determine cut point

Category: 
Loop Modeling

I am attempting to update my group's GPCR loop modeling protocol to utilize the LoopModeler mover (rather than using the unmaintained LoopRelaxMover as we have been) and am running into errors regarding loop cut points. My XML file is as follows:

Post Situation: 

What is a rational minimal value for the "-nstruct" option

Category: 
Loop Modeling

Dear all,

I am using the "antibody_H3" command to model the H3 loop of antibodies according to the guide at https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol.

Post Situation: 

can remodel add loops in one chain in multichain PDB structure?

Category: 
Loop Modeling

I'm trying to model 4 loops within each of 4 chains within one PDB file. Modelling the loops simultaneously is important because all chains (and also 4 another without any loops to model but interacting with that 4 remodelled) are assembled into oligomer, so that loop formation should take into account other chains. I have:

Post Situation: 

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: 

Pages

Subscribe to RSS - Loop Modeling