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How to apply cartesian_ddg to multi-metric enzyme?

Submitted by Wang Zhe on Wed, 2021-12-08 10:07
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.

 

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Rosetta 3 - Applications

connecting pdb files

Submitted by Hyun on Wed, 2021-11-17 22:32
Category: 
Design

Hi

I has been using RosettaRemodel -remodel:domainFusion:insert_segment_from_pdb for connecting pdb files such as connecting 1 helix pdb file and another 1 helix pdb file.

But it doesnt always work, is there another way to connecting two helices in different pdb file by loop? 

Im wondering what protocols can be used for connecting two pdb files with loop to generate 1 pdb file 

please help me 

Thanks

 

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Rosetta 3 - General

Help with file in article Kemp elimination catalysts by computational enzyme design

Submitted by Wenithor on Sat, 2021-10-09 07:23
Category: 
Design

Hello, I would like to ask for some help, regarding the article Kemp elimination catalysts by computational enzyme design, you would still have the transition state calculated by gauss, I need the output because I am trying to replicate the article, and I need the coordinates of the hydrogen being removed from the carbon in the transition state. Does anyone have these outputs?

Att. Thank you

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Rosetta 3 - General

pmut and scoring

Submitted by ldlamini on Tue, 2021-09-14 00:46
Category: 
Design

Hello all,

I am doing semi-rational design of my protein. So far I have one mutation that increases thermostability identified in vitro. However, Rosetta didn't predict this mutation in pmut scan. When I scored the protein variant with this mutation, the score was better than all the mutations predicted by Rosetta.

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Rosetta 3 - General

the question about ddg of disulfide bond mutants

Submitted by asbelx on Sun, 2021-08-29 06:40
Category: 
Design

I want to evaluate the ddg between WT and  disulfide bond mutants 

1. I try to use ddg_monomer and fond it does not suport it

2. Then I build disulfide bond mutants with moddler, and then  try to use ddg_monomer to evaluate  the ddg ( mutant  CYS  recovery to the amino acid of WT), and it does not work , too.

3. Just as 2.  I try to use another APP, cartesian_ddg ， and  disulfide bond mutants as the star model，and  ddgs seem is similar(just try three mutant)

 

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Rosetta 3 - General

Topobuilder segmentation fault

Submitted by tatsiana.bylund on Mon, 2021-08-09 07:10
Category: 
Design

I'm following the steps here https://github.com/LPDI-EPFL/topobuilder/tree/releasepy2 and got all the folders with different topologies, but once I'm in the folder and running submiter.sbatch, make_fragments protocol exits with a segmentation fault. 

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Rosetta 3 - Applications

How to make .frags files

Submitted by krosika1 on Thu, 2021-07-08 18:16
Category: 
Design

Hello! 

I am working through the online pyrosetta tutorial in jupyter notebooks, and they request you use files that are ".frags" files for ab initio structure prediction. Unfurtunately, all of the google drive files that come with the tutorial are no longer accessible (the link goes to a 404 error).

How do you create these .frags files for your POI? I tried using old robetta, but none of the "fragment" files produced have the .frags extension, nor can any of them be downloaded off of the internet. I would appreciate any help/advice!

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PyRosetta - Scripts

Rosetta Double changing mmCIF chain ID

Submitted by Victor Tobiasson on Thu, 2021-05-13 07:57
Category: 
Design

Hi everyone!

Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?

Best and thank for any help,

Victor

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Rosetta 3 - General

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