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Rosie vip function fails on multiple tries

Category: 
Design

Hi:

 

I can not get the rosie server vip function to complete.  After many hours it always ends with

 

VIP Job vip put cds 81q1 prepared pdb 「№72207」 Details

 

this error :

 

Job 「№72207」has failed with the message:

JOB FAILED: Scripts failed to produce HPC jobs json file...

 

Have tried several times now, thanks for any advice

 

- Amy F

 

Post Situation: 

Updating databases and weekly update

Category: 
Compilation

Hi,

I already have rosetta compiled in my linux workstation and it is working fine. Few questions regarding  regular updating of databases. How should I update the databases of rosetta. I know that there are weekly release for rosetta updating these release is enough. whether the weekly release has all the relevant updated database.   How  do I update the rosetta. Whether I have to recompile the source code from the weekly updates. These are very basic questions and your response will be greatly appreciated.

Thanking you

Post Situation: 

Enzyme Design FlexBB Protocol Bug: DNA/RNA handling

Category: 
Enzyme Design

Hi Folks,

I've been playing with the enzyme design binary application using enzymes containing DNA or RNA in the pose. The FlexBB protocol can be activated by setting the flag '-enzdes:flexbb_protocol true'. If no loop file is provided via the flag '-enz_loops_file <file>' the default  protocol behavior is to iterate through the pose to identify flexible regions in the structure for loop design. I found that having either DNA /RNA  in the pose triggers the following error consistently after cst minimization. 

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Hydrogen bond detection and shape complementarity

Category: 
Docking

HI,

I have PDB strucures of antigen- antibody complexs. want to studythe hydrogen bond pattern at the ineterface and also the shape complimentarity. As per the following manuscript (Kuroda et al, (2016) Bioinformatics, 32(16):2451-2456) the command line

report_hbonds_for _plugin.linuxgccrelease

-s

-prevent packing true

sc.linuxgccrelease

Post Situation: 

Question about fastsaxs and saxs_score

Category: 
Scoring

Hi,

I am trying to incorporate saxs score to my calculation, from some digging into this forum I got that fast_saxs term calculate the SAXS scattering curve from fullatom protein model and saxs_score term would calculate the curve from centroid-based model. My question is, can it work on heavy atom and nucleic acids? Thanks in advance...any comments or suggestions would be appreciated!

Orion 

Post Situation: 

Docking results

Category: 
Docking

hi

I am docking an antibody to antigen using the snugdock server. Just wanted to know whtat is the reference structure in the the RMSD deviation in the score.sf files. Is it the structure with the lowest rosetta energy. In case if you want to compare the original structure of complex with decoy structure what is the easiest option. i am attaching the gnuplot out put of the Total Score Vs RMSD  . Any help would highly be appreciated

Dr. Suji george

   

Post Situation: 

How to run PLOT LHOC on Results from Rosie Server

Category: 
ROSIE

Hi,

 I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.

Thanking you

Dr. Suji george  

Post Situation: 

Membrane ab-initio modelling of a beta-strand

Category: 
Structure prediction

Hello everyone!

We're trying to model a membrane peptide of ~50 aminoacids which likely assumes beta-strand conformation in the membrane. Can we do this with the current Ab Initio membrane implementation of Rosetta? I know that we should use Octopus to generate a span file, but I'm left with the impression that it's designed for alpha helical proteins and that Rosetta in general is biased toward generation of alpha helices. Is there a way to enforce some beta-sheet restrictions during the ab initio folding process?

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