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Mutations are ignored (fixbb) when using -auto_setup_metals option

Submitted by hdelrisco on Wed, 2019-06-19 15:43
Category: 
Design

When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).

Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals

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Rosetta 3 - General

VH-VL Orientation in antibody

Submitted by sujigeorge1979 on Mon, 2019-06-17 01:23
Category: 
Structure prediction

 

How to determine the VH-VL orientation angle in rosetta. i came across this manuscript "Improved prediction of antibody VL–VH orientation" by Protein Eng Des Sel. 2016 Oct; 29(10): 409–418. Here there is description of MT protocol. Whether the script is provided in the rosetta 3.1 version. Or is there any other alternative in rosetta to calculate the VH-VL orientation (LHOC) angle of antibody in rosetta.

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Rosetta 3 - Applications

Rosie vip function fails on multiple tries

Submitted by Amy F on Sat, 2019-06-15 12:51
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

 

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ROSIE - General

Updating databases and weekly update

Submitted by sujigeorge1979 on Fri, 2019-06-14 21:26
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

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Rosetta 3 - Build/Install

Enzyme Design FlexBB Protocol Bug: DNA/RNA handling

Submitted by kettner on Fri, 2019-06-14 14:16
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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Rosetta 3 - Applications

Hydrogen bond detection and shape complementarity

Submitted by sujigeorge1979 on Fri, 2019-06-14 02:39
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

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Rosetta 3 - General

Question about fastsaxs and saxs_score

Submitted by orionshih on Thu, 2019-06-13 02:30
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 

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Rosetta 3 - Applications

Docking results

Submitted by sujigeorge1979 on Wed, 2019-06-12 23:40
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

   

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ROSIE - General

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