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Comparative Modeling Tutorial Script not working

Submitted by Srinivas23 on Thu, 2017-09-21 12:00
Category: 
Structure prediction

Hi All,

I am trying the tutorial of Comparative Modeling using Rosetta and I am not able to run this script  (<path-to-Rosetta>/Rosetta/demos/tutotial/rosetta_cm/scripts/clean_pdb.py 2RH1_ISOLATED A). The "path-to-rosetta" in my Mac is "Applications" and also I have the latest python version. Does the scripting change with python versions as well?? Any help in this regard is greatly appreciated.

Thanks

Srinivasan Krishnan

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Rosetta 3 - General

Abinitio Video

Submitted by ac.research on Tue, 2017-09-12 04:00
Category: 
Structure prediction

Dear All (especially rmoretti - because you seem to know everything),

 

I am thinking of making a video about how to use Rosetta Abinitio (a video tutorial). Would there be any breach of licence somehow, or is there anything that says I should not make an explanatory (tutorial) video and publish it on youtube? I have not yet decided which .pdb structure to use (still looking for something that shows a good funnel plot).

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Rosetta 3 - General

Relax is resulting in a Segmentation Fault

Submitted by brspurri on Thu, 2017-08-24 18:46
Category: 
Structure prediction

First off, I hate to be asking about a "Segmentation Fault" here because I know it can be any number of things; but I'm completely stuck and need to ask for help.

I am preparing a structure for downstream modeling, and I am running a very simple relax following the steps outlined here (the short protocol):

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Rosetta 3 - Applications

Getting error with Rosetta "antibody.linuxgccrelease" command

Submitted by Sunyp_IM on Mon, 2017-08-07 19:40
Category: 
Structure prediction

Dear all, 

I installed ROSETTA3 (rosetta_src_2017.08.59291_bundle) on my centos 7 system. The install process seemed ok without error.

when I use the antibody.linuxgccrelease to prediction antibody structure according to the tutorial in the Nature Protocol 2017, 12(2),401 paper with the follow commad:

antibody.linuxgccrelease -fasta antibody.fasta -exclude_homologs -exclude_homologs_cdr_cutoff 95 -exclude_homologs_fr_cutoff 90 -antibody::grafting_database $ROSETTA/tools/antibody | tee grafting.log
 

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Rosetta 3 - Applications

Antibody prediction with ROSIE failed

Submitted by Sunyp_IM on Wed, 2017-08-02 23:45
Category: 
Structure prediction

Dear all,

I submitted the sequeces for the variable regions of the heavy and light chains of a antibody to ROSIE in order to predict the 3d structures. However when the job finished there seemed no structure output. The following is the output message:

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ROSIE - General

Problem with the top 25 fragments used in the library of 200 nine-residue fragments in AbinitioRelax

Submitted by MA on Wed, 2017-07-26 01:12
Category: 
Structure prediction

Hi,all.

I'm confused about the reason for using the top  25 fragments in the library of 200 nine-residue fragments in AbinitioRelax.Instead,for the library of 200 three-residue fragments,all fragments are applied in the process of fragment assembly.

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Rosetta 3 - General

Problem with outputing decoys in the process of AbinitioRelax

Submitted by MA on Thu, 2017-07-13 23:27
Category: 
Structure prediction

Dear all,

I am new to rosetta and trying to record the information in the process of AbinioRelax followed by analysis. In this case,it's necessary to output plenty of decoys generated after fragment assembly.However,I can't output these decoys to just one file.Using the function "pose.dump_pdb()",I can output them to mutiple .pdb files,which is  not convenient and take too much time.

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Rosetta 3 - General

Did RosettaScripts recently switch to fully parallel MPI?

Submitted by beowulfey on Thu, 2017-07-13 09:02
Category: 
Structure prediction
Design

Hi, trying to figure out if something isn't working properly or if it's working as intended and I missed it. I was using the Topology Broker via Rosetta Scripts from the 2016/Week 46 build of Rosetta and when I ran my script via MPI, it would create one nstruct per core, not including the controlling core. I was able to see this in the log; different commands were marked with (0), (1), (2) etc, for presumably which core the message came from. So if my command was: 

mpiexec -np 4 rosetta_scripts @flags -nstruct 10

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Rosetta 3 - Build/Install

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