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%time results = list(xml_obj(pose_obj)) error



When I ran the following syntax in this file, an error came out and it did not proceed.

if not os.getenv("DEBUG"):

    %time results = list(xml_obj(pose_obj))

I also set up Conda on Google Collabor
There is an error, do you know how to solve it?

The results of the implementation were as follows


Post Situation: 

Issues compiling Rosetta on stampede2


Hi everyone,

I am trying to compile rosetta3.13 on stampede2 using the SCons assistant as described in the documentation. 

I am using the command: 

./ -j1 bin mode=release bin extras=mpi

which has repeatedly given the error

Post Situation: 

Failure to produce a cst file


Hi, I generated a mincst.log using the below command:

minimize_with_cst.default.linuxgccrelease -s fe.pdb  -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database /home/protein-institute/ROSETTA/rosetta_bin_linux_2020.08.61146_bundle/main/database -ddg::harmonic_ca_tether 0.5 -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false > mincst.log

then produced mincst.log file was employed for generating a cst file as input for the high-resolution protocol of ddg_monomer using the below command:

Post Situation: 

Ligand Rotamer Control in Macther


I am trying to run matcher with several residue constraints, and have already benchmarked the constraints individually and combined. Problem is that my ligand has several rotamers and once I enable the rotamers consideration in the matcher, the match enumeration makes the run impractical. I could solve this by removing the ligand rotamer consideration for the constraints that don't need it. Is there a way to do this for individual constraints?


Post Situation: 

Setting pivots points for GenKIC

Non-Canonical Peptides

Hi all,

I want to use GenKIC to generate macrocycles of a peptide bound to a receptor with the anchor design approach. Previously, I used simple_cycpep_predict, from the command line, to generate the candidates, but not bound to the receptor.

Post Situation: 


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