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"ddg_monomer.linuxgccrelease" by following "High Resolution Protocol"

Category: 
Design

(I would appreciate it if any of the following can be commented)

Dear friends,
I am trying to use "ddg_monomer.linuxgccrelease" by following "High Resolution Protocol" in
https://www.rosettacommons.org/docs/latest/ddg-monomer.html

1. To pre-minimize, the command line is

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clustering

Category: 
Structure prediction
Design

Hi,
I have a couple of questions regarding Rosetta clustering and Calibur and I wasn't able to find an answer to them on the site
Which type of clustering algorithm is used in Rosetta clustering? EDIT:I meant to ask- when calculating the RMSD is the superimposing done pairwise in Rosetta clustering?

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Parse error while reading in XML file in ROSETTA Scripts

Category: 
Design

Hello everybody,

I wanted to run a ROSETTA Scripts script to design a portion of a protein interface. But I struggle with an unexpected error, which appears to occur during reading in the XML protocol. I started the application with the following command line:

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task_pack.restrict_to_repacking() not working

Category: 
Design

Dear Sir or Madam,
I am learning the "Monte Carlo Side-Chain Packing" in Workshop6.

After successfully typing

task_pack = standard_packer_task(pose),

I was trying to use

task_pack.restrict_to_repacking() .

However, I was told "MemoryError" (attached). Can someone tell me what is the reason? Thank you very much.

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mutate_residue not working

Category: 
Design

Dear Sir or Madam,
Can I ask how to properly use the command of
mutate_residue(pose, 49, 'E') ?

It seems to be quite straightforward as pose name, residue number and amino acids are included into the parenthesis. However, I have been told
"MemoryError" (attached) after typing

from toolbox import mutate_residue
mutate_residue(A10, 3, 'E')

Do I need to type something else before using this command?

Basically, I want to mutate several amino acids into customised ones. Is this the best way to do?

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HBNet and RosettaScripts

Category: 
Design

I recently learned about a new Rosetta module for scoring hydrogen bond networks as part of protein design called HBNet. I was interested in trying out this module but I'm not sure how to use it. Recently I compiled one of the weekly releases of Rosetta3.5 so I think we have the most up-to-date software. HBNet is a RosettaScripts module I believe but I was wondering if someone could provide a sample XML script that I could play around with if it is not too much trouble. Thank you for your assistance!

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Remodel: neighbor cutoff

Category: 
Design

Hi

I am trying to design and sample a loop using Remodel. Residues that are interacting but farther away than 6 A are not being repacked (using the -find_neighbors) and I would like to increase the cutoff. How can I change this parameter?

thanks in advance

felipet

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FloppyTail vs. Remodel for linkers

Category: 
Design

I have a 11aa long linker (known sequence) connecting two parts of a protein (NOT two independent domains). I want to model the linker before some downstream Rosetta analysis on the protein. It seems FloppyTail is often suggested for the modeling of linkers.

My question is: how is FloppyTail compared to Remodel + Fixbb? What if I just insert some 11aa long extension (of any sequence) between the two parts using Remodel, then I use fixbb to mutate this newly inserted extension to the sequence of my linker? How would this compare to FloppyTail?

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Failed glycine check when running RosettaRemodel to build disulfide

Category: 
Design

Hi Rosetta users,

I was recently running RosettaRemodel to build a disulfide between two residues. The first residue is a gly and the second is tyrosine. I ran into this error:

"Failed glycine check. Cysteines cannot replace glycine positions in the native pose."

Is this because gly doesn't have a CB atom so that the CB-CB distance cannot be measured? I can think of mutating the gly to other residues as a workaround. But is there any other way to build a disulfide bond involving a gly using RosettaRemodel?

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