Using pyrosetta to generate quaternary structure of protein
Submitted by nasim.soltani58 on Thu, 2020-11-19 17:35
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Structure prediction
helical bundle predict
Submitted by ii_cnr on Fri, 2020-11-13 09:53
Category:
Compilation
Structure prediction
Hi everyone,
I'm interested in using the helical_bundle_predict method. In this link (https://www.rosettacommons.org/docs/latest/structure_prediction/helical-bundle-predict) it is described as an application but I cannot understand how to make the system install it. It may have something to do with the fact that it is a pilot application, but still it is not clear to me which files I need to modify in order to install it with scons.
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Using Rmsd RosettaScripts filter with alignment files
Submitted by bjharris on Sun, 2020-11-08 15:51
Category:
Structure prediction
I have a homology model that contains a residue insertion and thus a 1:1 residue RMSD calculation cannot be performed. I would like to try the Rmsd RosettaScripts Filter with an alignment file to get the correct C-alpha RMSD calculation. However, I'm not sure how to create this alignment file. I've tried the alignment Grishin file I used for Homology modelling but receive this error:
File: src/protocols/protein_interface_design/filters/RmsdFilter.cc:217
[ ERROR ] UtilityExitException
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Comparatively modelled chains are far apart in final structure while the template pdb has all chains in a close-knit complex
Submitted by Sunidhi on Sun, 2020-11-01 11:00
Category:
Structure prediction
I tried to model a protein sequence (4 chains) using RosettaCM. The structure of the protein is already available in PDB (2ERJ). The issue I am facing - the final modelled structure has all the 4 chains very far apart, unlike the pdb. What exactly is going wrong?
I am obtaining the alignment file from Clustal omega. The target fasta sequence is given as chain1/chain2/chain3/chain4 and the 2ERJ fasta is also given in the same format in clustal omega so that the final alignment has only 2 unique identifiers in the ali file, like this:
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Membrane Abinitio modeling error
Submitted by jkyan007 on Thu, 2020-10-29 03:30
Category:
Structure prediction
Hi,
I am modeling a 178 residue membrane protein sequence using the abinitio protocol
To briefly describe what I have done:
1. generate structure fragments using Robetta server
2. generate a span file using OCTOPUS server and the script, octopus2span.pl
3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl
4. generate PDB using membrane_abinitio2.linuxgccrelease
I can run the BRD4.fasta in the tests successfully following above protocols.
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Extracting PDBs from a Silent file: "Can't find residue type for ARG"
Submitted by avsrivatsa on Sat, 2020-10-17 16:20
Category:
Structure prediction
Hello everyone,
I am refining protein structures into Cryo-EM maps, and my output is a silent file. Currently, I am attempting to extract the pdbs from the silent file so that I can analyze and score the structures. The protein has a missing loop, and it is failing on the C-terminus right before the missing loop. Specifically, my error for each structure is "ERROR: can't find residue type for ARG:CtermTruncation at pos 114 in sequence G".
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not knowing which one of three ways to run rosettascript
Submitted by xinmiaohe on Tue, 2020-10-13 13:52
Category:
Structure prediction
Hello,
I meet a question when I am to run rosettascript. I found three executables but I do not know which one to choose. I am wondering whether some one can help me out. I would be much appreciated.
I found three ways, as below, to run rosetta scripts I am wondering what are differnece in these three executables. Will they give same results for the same inputs. whether settings are same in these three ways.
rosetta_scripts.default.linuxgccrelease
rosetta_scripts.linuxgccrelease
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Robetta ab initio - TrRosetta for membrane proteins
Submitted by benhardy on Wed, 2020-09-30 08:42
Category:
Structure prediction
Membrane
Hi All,
I'm looking for some clarification of how the Robetta server, and specifically the new TrRosetta algorithm, deals with structure prediction for membrane proteins.
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RosettaCM or FastRelax?
Submitted by Tianyang89 on Wed, 2020-09-23 07:46
Category:
Structure prediction
Hi,
I have a Cryo-EM density and AA sequence for a protein , but the density is not good enough for assign the residues unambiguously.
I'm particularly interested in one alpha-helix and based on secondary structure prediction, I have roughly known the AA sequence for the helix.
But the secondary structure prediction can't tell the boundary of the helix unambiguously.
Could anybody have any ideas about how I can get the correct register for the helix using Rosetta???
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4mer 6mer fragment database
Submitted by bjharris on Wed, 2020-09-09 15:12
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