RemodelMover and Input Pose
Submitted by ozyo on Tue, 2020-12-29 09:41
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Loop Modeling
De novo backbone trace from fragments
Submitted by Victor Tobiasson on Tue, 2020-12-22 06:34
Category:
Structure prediction
Design
Loop Modeling
Dear Rosetta experts,
I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.
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Error when using Remodel on a protein with a chemically bound ligand
Submitted by Pappmaschee on Wed, 2020-12-16 09:23
Category:
Loop Modeling
My goal is to insert a linker fragment into a protein which has a chemically bound ligand. To do that, I have relaxed the structure with the chemically bound ligand and am now trying to insert the linker fragment into my protein using Remodel. The ligand is bound to a CYX residue (modified Cystein) in my protein.
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loop modelling on complex structure
Submitted by Tianyang89 on Fri, 2020-09-18 07:24
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
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Does antibody_numbering_converter support camelid antibody?
Submitted by mxp on Tue, 2020-07-07 01:21
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:
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Building loop extensions in a membrane protein with Remodel
Submitted by benhardy on Tue, 2020-06-02 08:21
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:
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LoopModeler mover unable to determine cut point
Submitted by gszwabowski on Mon, 2020-06-01 13:12
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:
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What is a rational minimal value for the "-nstruct" option
Submitted by Sunyp_IM on Fri, 2020-05-22 01:28
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.
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can remodel add loops in one chain in multichain PDB structure?
Submitted by ksteczk on Fri, 2020-05-01 06:26
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:
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Is cis-Glycine okay?
Submitted by matteoferla on Tue, 2019-11-19 07:26
Category:
Loop Modeling
Yes, that is not a typo for cis-proline! I don't have an issue just curious. I have a loop that Rosetta Remodel (all PIKAA entries) is struggling with despite the generic_aa set to G (but most likely for biological reasons), which got me thinking...
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