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The problem hasn't been solved
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.
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:
- Relax the whole enzyme, calculate each chains' ddg, and finally average the numbers.
- Split the enzyme complex into subunit monomers, calculate each monomers' ddg, and finally average the numbers.
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:
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 ]
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 ?
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.
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!