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How to determine interface residues

Submitted by rbehan on Wed, 2015-10-14 11:25
Category: 
Scoring
PyRosetta

Hi,

I have a couple questions about fold-trees and how interfaces are calculated in pyrosetta (or rosetta).  I have a structure of an antibody-antigen that I have prepared using rosetta (attached).  A visual inspection shows that residue B:TYR210 is making a number of close contacts with residues in Chain C (the antigen).  However, when I construct an Interface object in pyrosetta, this residue is not identified as being in the interface (using a cutoff of 5.0A):

 

from rosetta import *

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PyRosetta - General

The following options have been set but have not yet been used

Submitted by jrcf on Fri, 2015-10-09 10:48
Category: 
Structure prediction

Hi guys...

I'm using the Basic Homology Modeling, and received this massage on the final of the execution.

protocols.jd2.JobDistributor: WARNING: The following options have been set, but have not yet been used:
        -in:file:frag3 3rvyCH1_03_05.200_v1_3
        -in:file:frag9 3rvyCH1_09_05.200_v1_3
        -in:file:psipred_ss2 3rvyCH1.ss2
        -loops:frag_files  3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none
        -out:output 
        -out:pdb 

Here is my script

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Rosetta 3 - General

pose.replace_residue() & incorrect scoring

Submitted by msun on Tue, 2015-10-06 10:51
Category: 
Design
Scoring

Hi developers,

I wasn't sure where to submit bug reports so I'm posting here instead.

I've noticed a scoring error after repeated pose.replace_residue() function calls. The final pose after repeated calls to replace_residue() ends up having a score substantially lower (often < -50 Rosetta energy units) than when scored using the scoring application or if the pose is loaded upon application initialization.

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PyRosetta - General

Rosetta Holes

Submitted by zsun12 on Wed, 2015-09-30 11:40
Category: 
Scoring

Dear Rosetta Users:

I would like to use the rosetta holes application to evaluate the packing of my protein. But the documentation for this aplication is not in great details. I have been searching posted questions about rosetta holes from the forum and it seems that this app has been in and out of the rosetta suite. So I am wondering if the rosetta holes is currently available in the most updated rosetta version and if there is a general guide on how to use this application.

Thank you very much!

Best regards,

zsun12

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Rosetta 3 - Applications

Ways to improve ROSIE docking2 jobs

Submitted by AdoCbl on Wed, 2015-09-23 15:12
Category: 
Docking

(1) By the images of various output pdb files, be more clear that these are ones with the ten lowest I_sc (interface energy) scores.

(2) In the instructions, give more details about the differences between local_docking and docking_local_refine protocols.

(3) For each docking_local_refine job, please let every output pdb file listed in score.sf have a unique name and include all these pdb files in the tar archive file for the job.

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ROSIE - General

Ways to improve both docking2 and symmetric_docking jobs

Submitted by AdoCbl on Wed, 2015-09-23 14:43
Category: 
Docking

(1) When you click on a point in a plot, a window appears listing data for that point. Often the cursor blocks the top line of this window. Could you add a blank line to the top of this window so the cursor doesn't block any important data?

(2) Could you prevent job names from ending with blanks, /, or \ characters? I have tried automatically fishing results out of the resultant tar files using Matlab, but Matlab has given trouble when the job names end with blanks. I'd imagine job names with / or \ in them could cause similar problems.

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ROSIE - General

Ways to improve ROSIE symmetric_docking jobs

Submitted by AdoCbl on Wed, 2015-09-23 13:39
Category: 
Symmetry

Below are some ideas for improving symmetric_docking jobs:

(1) If you choose dihedral instead of cyclical symmetry, it seems like you also need an even number of subunits. Could you have the input page block dihedral jobs with odd numbers of subunits?

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ROSIE - General

Transitioning from ROSIE to Rosetta

Submitted by AdoCbl on Wed, 2015-09-23 11:49
Category: 
Compilation

I have been using ROSIE for a while now and am wondering what is the easiest way to transition to Rosetta. For example, is the code needed to make all the files in the tar archives for ROSIE docking2 and symmetric_docking jobs available? If so, where can I find this code? Is this code included in some of the many files included in the tar archives ROSIE makes for each job? If so, which files? It would be great if I could start with this code and adapt it as desired to do more complicated things in Rosetta.

Thanks!

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ROSIE - General

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