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Installation files not found

Category: 
PyRosetta

I'm currently installing PyRosetta on windows (anaconda) using the linux tar file with the installation instructions from

http://www.pyrosetta.org/dow

I've reached step 6:

From within the new PyRosetta directory, type cd setup && python setup.py install into the command line to set up the PyRosetta.

I've run the installation and received the following output:

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Noob question about optimizing a pose

Category: 
PyRosetta

Hello, I am very new to PyRosetta, so this might not make a lot of sense. What I'm trying to do is minimise the energy of a given pose. I don't know much about this, so any tips about how to approach it and which instruments to use would be appreciated. Thank you.

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Ligand Binding

Category: 
Docking

Dear Ligand binding Team,

I am writting this letter of appreciation to thank the team of Rosie Ligand Docking for making available such a powerful docking tool for researchers. We recently used the tool and got wonderful results using a difficult protein (oxidosqualene cyclase). We also want to thank you for making rarely available docking tool based on Induced-Fit freely available to academic users.

We hope that you continue providing the Rosie tools and keep updating the excellent Ligand Docking tool.

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Rosetta params for taxol

Category: 
Structure prediction

I want to use RosettaCM for density guided homology modeling. My structure contains taxol and other ligands: GTP and GDP, but my /rosetta/main/database/scoring/score_functions/facts contains params files for just GTP and GDP but not taxol. I atatched my taxol.pdb file for reference. 

Thanks in advance. 

 

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Error with simple_cycpep_predict protocol while using a native pdb file

Category: 
Structure prediction

Hello Rosetta devs,

 

I'm not sure that this is the right place to post a bug. If not, please let me know where to post.

 

I compiled both Rosetta 3.10 (and then 2019.07 release), and faced the following error when trying to predict cyclic peptides with terminal disulfide bonds using the simple_cycpep_predict protocol.

To be more specific, my peptide has a non-terminal CYS residue at the C-term, and I was using the

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Abinitio the Broker protocol

Category: 
Structure prediction

Hello everyone,

I am reading about the Abinitio protocol to see how I can include a checkpoint file in the Abinitio flags, but i could not find any information on how to input a checkpoint file. so this is my question:

  • can I input a checkpoint file into Abinitio? if i can what is the flag     -in:file:  ?

 

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ProteinInterfaceDesign algorithm questions

Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro.  Thanks in advance

        </SCOREFXNS>

        <FILTERS>

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make_fragments.pl

Category: 
Fragment Generation

Hi everyone,

           I wanted to let you know about a bug that I was able to fix. if you use the make_fragments.pl in the /rosetta/tools/fragments/ folder it calls another script install_dependencies.pl it calls an online script update_blastdb.pl which in the install_dependencies.pl is at this url:

 

https://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl

 

it returns a 404 error. 

 

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