Movers for unspecified DoF
Submitted by tfobe on Wed, 2019-04-17 17:30
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input file for loop modeling
Submitted by Negarsardar on Tue, 2019-04-16 10:21
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?
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newbie question re pose syntax
Submitted by Amy F on Mon, 2019-04-15 12:50
Category:
PyRosetta
Hello :
I am learning the basics of pyrosetta from this tutorial
https://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Manual.pdf
but when I enter the code verbatim I get an error.
is something wrong with the syntax they give? trying to do this:
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The question about FavorNativeResidue
Submitted by asbelx on Fri, 2019-04-12 20:02
Category:
Enzyme Design
I read the paper Rosetta and the Design of Ligand Binding Sites doi:10.1007/978-1-4939-3569-7_4.
then try to use EnzRepackMinimize to design the protein.
But FavorNativeResidue was set as 0.5-3.0, the mutant position numbers are same and there are too many mutant positions.
However, I use the PackRotamersMover by changing FavorNativeResidue and can get different mutant position numbers.
How can I solve it? Thanks.
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is it necessary to always run relax before any Rosetta
Submitted by mainzer on Fri, 2019-04-12 01:35
Category:
Design
I performed p_mut_scan to see if certain mutants make the protein more stable. Is it absolutely necessary to run Relax (1) before running anything [2] like pmut_scan or ddg_monomer. I have already done about 6 months of work with these without Relax. Surprisingly, pmut_scan did correctly predict 2 mutants.
-> Do I have to redo everything since I did not relax the structure?
->Another question: What is the meant by "options_annealer" section in the documentation: " By default, fixbb uses the standard annealer used" [3]
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problems with implementing NOE constraints
Submitted by connyyu on Thu, 2019-04-11 12:37
Category:
Constraints
Hi I'm running csRosettaCM with POMONA alignments and I would like to include NOE constraints in my models. Some of my constraints are on the side chains, therefore I cannot implement them in centroid mode, and would like to implement them in the full atom mode. However, it seemed like csRosetta has ignored my cst_fa_file and did not take in the constraints on the side chain. Any suggestion on how to fix this? And if it is possible to run csRosetta in full atom mode directly?
I have the following in my flags file:
-cst_fa_file noe_fa.cst
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protocols.jd2.JobDistributor: [ ERROR ]
Submitted by johnnytam100 on Thu, 2019-04-11 09:30
Category:
Design
Hi I met the error "protocols.jd2.JobDistributor: [ ERROR ] " when I run antibody_designer of RAbD, that I tried to use 3ogo.pdb (renumbered with PyIgClassify), which is a nanobody-antigen complex structure, as input.
Has anyone come across the same error before?
My command was:
/home/cltam/Desktop/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/antibody_designer.static.linuxgccrelease -s 3ogoOut.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -allow_omega_mismatches_for_north_clusters
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Error when trying to import 'get_secstruct'
Submitted by quantumnumber on Thu, 2019-04-11 03:50
Category:
PyRosetta
Hello everyone,
I just installed and started playing around with PyRosetta, following the corresponding workshops in the web page, when I got the following error:
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Protein Protein Docking with Constraints
Submitted by ajaniharesh on Wed, 2019-04-10 07:26
Usage of the TaskOperations "RestrictToCDRsAndNeighbors"
Submitted by johnnytam100 on Wed, 2019-04-10 02:58
Category:
Design
Hi, I would like to include the TaskOperations "RestrictToCDRsAndNeighbors" in my xml file which is to design the CDR in an antibody-antigen interface.
However, I do not know what to put as options under the arguments "numbering_scheme" and "cdr_definition"
From the manual, the explanations are
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