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individual residue score

Category: 
Scoring

Hi all,

I just have a question about the individual AA score. So I am trying to compare the total score (with proper weighted scoreterms) and the individual AA score. 

For the total score I used:

scorefxn = get_fa_scorefxn()

score = scorefxn(pose)

To get the weighted indicidual AA score I used:

pose.energies().residue_total_energy(residue#)

 

Post Situation: 

Sampling a wider range of RMSD of poses by Rosetta Dock

Category: 
Docking

Hi, I am designing a protein interface of a nanobody with my target antigen.

1000 initial poses were generated by patchdock and 1000 designs were generated per each pose.

After ploting the ddg-rmsd scatter plot, I found all the poses has a characteristic scatter plot like fig. A attached (a narrow RMSD range within ~0.25A, while a majority stays exactly at 0.00A).

Post Situation: 

Relax with constraints

Category: 
Constraints

Hi everyone,

I am a newbee in Pyrosetta, and I am trying to learn how to relax with constraints. I wanted to do distance constraints, but I am not sure if I am doing it right or wrong at all.  The score came out to be almost the same for with and without the constraint. Can anyone give me any advise? 

#------------------------Set up Score Function-----------------------

scorefxn = get_fa_scorefxn() 
score_before = scorefxn(pose)

Post Situation: 

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:

Post Situation: 

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.

Post Situation: 

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.

Post Situation: 

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. 

 

Post Situation: 

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

Post Situation: 

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:  ?

 

Post Situation: 

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