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Structure prediction

antibody.linuxgccrelease- output models don't have the same sequence as the input fasta

Category: 
Structure prediction

hi,

I am using antibody.linuxgccrelease aplication in order to model camiled heavy chain only antibodies.

when using the command:

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta my_fasta.fa | tee grafting.log

 

for example with my_fasta.fa:

Post Situation: 

RosettaAntibody - No matching templates for CDR1

Category: 
Structure prediction

hi,

I am trying to use RosettaAntibody in order to model a camiled heavy chain only antibody (pdb code: 1YC7_1).

when using the following command:

antibody.linuxgccrelease -exclude_homologs true -vhh_only -fasta 1YC7_1.fa | tee grafting.log

(I am using exclude_homologs in order to test its preformance, because this antibody structure is already solved and found in the database).

I get the following error:

Post Situation: 

relax.linuxgccrelease in multiple processors

Category: 
Structure prediction

Hi, sorry if my question is naive.  But I would like to aks if it is possible to run  the next command in multiple processors and not in just one?

relax.linuxgccrelease -s model1.pdb -nstruct 1000

 

regards

and thank you

Post Situation: 

[Solved] RosettaAntibody3 - Grafting step is failing to detect H3 from the input sequence

Category: 
Structure prediction

I am trying to run RosettaAntibody3 to build an Fv hhomology model from an input sequence. I am following the documentation form here.

I am using the command: 

antibody.static.linuxgccrelease \
  -database $ROSETTA_DATABASE \
  -fasta /mnt/data/input/myinput.fasta \
  -nstruct 1 \
  -out:path:all /mnt/data/output/output-graft/ \
  -detect_disulf false

 which fails fairly quickly with the error:

Post Situation: 

De novo backbone trace from fragments

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.

Post Situation: 

helical bundle predict

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. 

Post Situation: 

Using Rmsd RosettaScripts filter with alignment files

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

Post Situation: 

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