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compiler option not found

Category: 
Compilation

Hi all,

I recently had to update my OSX command line tools and in doing so went from clang 12.0 to 13.0

I'm trying to compile Rosetta build 2021.16.61629 and am running into an issue. I was previously able to compile fine with clang v12.0.

As far as I can tell there seems to be an issue with the -rpath option, but that doesn't make much  sense. See the fail point and error messages below.

Not sure if this is a zlib issue given the fail point. As far as I can tell I have zlib installed properly. 

 

Post Situation: 

How to apply cartesian_ddg to multi-metric enzyme?

Category: 
Design

Hello,

 I would like to compare stability of the wild-type and mutated proteins(multi-metric enzyme) using cartesian_ddg. But I am confused about which one is suitable structure input. And I have two ideas now:

  1. Relax the whole enzyme, calculate each chains' ddg, and finally average the numbers.
  2. Split the enzyme complex into subunit monomers, calculate each monomers' ddg,  and finally average the numbers.

 

Post Situation: 

Relaxed proteins show higher clash score in molprobity results.

Category: 
Structure prediction

Hi everyone,

I am tring to refine the predicted structure from alphafold and SWISS-MODEL database. Since the protocol I followed said I need to eliminate the steric clash and do refinement in predicted structure first (and then docking or some other analysis).

So I just relaxed protein in torsion space with constraints. And here is the code I used:

Post Situation: 

Question about running scallo

Category: 
Scoring

 I am trying to run code on https://github.com/strauchlab/scaffold_design

but it occur an error :

basic.io.database: [ WARNING ] Unable to locate database file scoring/score_functions/aa_composition/%%aa_comp%%.comp
Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'startingstub_0000_0008_0001'
Error: [ ERROR ] 

Post Situation: 

Downloading Rosetta weekly release

Category: 
Compilation

Hi guys,

I tried to download the most recent release of Rosetta.

However, from what I checked on this website the last one is of September 2021

(Rosetta 2021.38 : https://www.rosettacommons.org/downloads/academic/2021/wk38/).

Is there more recent version?

I guess the weekly relases can be downloaded from somewhere else ?

Post Situation: 

pyrosetta.rosetta.core.pose.rna

Category: 
Structure prediction

hey,

Enclosed the final model and problem. I use the pyrosetta.rosetta.core.pose.rna to build RNA 3D strucutre. When I check the final results, I found that 

the base part is not connected to backbone.  I want to know how to solve this problem.

Best wishes,

Chenjie

Post Situation: 

Rosettasurface in Pyrosetta 4

Category: 
Docking

Greetings,

    I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.

    Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4? 

Thanks very much!

Hao

Post Situation: 

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