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membrane ab-initio modeling, is the quality comparable to comparative modeling of 20% id template?

Submitted by fglaser on Thu, 2011-04-07 07:57

Dear All,

I would like to try your membrane ab-initio modeling protocol of rosetta, to model a membrane protein of 6 TM regions. But I am not sure how your protocol should perform compared to homology modeling, this protein has 370 aa and has a distant template of about 20% id for 300 aa region. I wonder if rosetta ab-initio method could produce equivalent or better results than the comparative modeling based on the template we have, and what is the best course to follow. And wether or not the results will be comparable.

Best regards and thanks a lot,

Fabian

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Rosetta 3 - Applications

How to build a parallel version of rosetta++(Rosetta 2.3.0)???

Submitted by ice_flame on Fri, 2011-03-25 22:24

Hi Rosetta users,

I'm using Rosetta 2.3.0. I want to build a parallel version. I installed MPICH and scons and modified some lines of basic.setting which is in rosetta++/tools/build/. I added the mpi bin, include amd lib path to the file and added a flag "Wno-long-long" to make mpicc and mpiCC work (since the cpmpiler always complains about that it doesn't support 'long long' type). I also installed the rsh-version and configured it to make the work.

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Rosetta++ - Build/Install

How to build a parallel version of rosetta++ (Rosetta2.3.0) ?

Submitted by ice_flame on Fri, 2011-03-25 22:20

Hi Rosetta users,

I'm using Rosetta 2.3.0. I want to build a parallel version. I installed MPICH and scons and modified some lines of basic.setting which is in rosetta++/tools/build/. I added the mpi bin, include amd lib path to the file and added a flag "Wno-long-long" to make mpicc and mpiCC work (since the cpmpiler always complains about that it doesn't support 'long long' type). I also installed the rsh-version and configured it to make the work.

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Rosetta++ - General

the meaning of total_score in docking

Submitted by libai2098 on Mon, 2011-03-21 05:46

Now,I use Rosetta for protein-protein docking.But I do not understand the meaning of total_score .-270 is better than -280?I think the Rosetta manual is not very perfect.What is more,Fnat , I_sc ,Irms, fa_ hack,interchain_contact are not write in manual.I will look forward to your response.Thank you.

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Rosetta 3 - Applications

Re-building protocol crash

Submitted by murgantia on Sun, 2011-03-13 05:28

Dear all,
I'm trying to using rosetta to execute following protocol:

aa t000 _ -relax -looprlx -nstruct 10 -fa_input -use_sspair -random_loop -termini -idl_no_chain_break -loop_skip_rate 0.0 -vary_omega -l pdbs.list

but after creation of 1-7 on 200 decoys roserra crash with this error:

WARNING: pose::set_fold_tree reordering tree at 1
bad fold tree!

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Rosetta++ - General

Minimization Toolkit W/GUI

Submitted by jadolfbr on Sat, 2011-03-12 15:58

jadolfbr, 2013 - Please do not use this GUI. It was a beta version of an expanded PyRosetta Toolkit GUI which should be released in Rosetta Version 3.5.

Hi All. Just wanted to share part of an application that I've been working on. It is a Tkinter application for use with Minimization of Proteins and Loops.
It uses the Rosetta Classic Relax, Fast Relax, dfpMin Minimization, and Sidechain movers.
Run it using "python Tkinter_Min_main.py" (All files need to be in the same directory, and the extensions changed to .py)

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PyRosetta - Applications

JobDistributor Bug

Submitted by brettth on Fri, 2011-03-11 07:00

I've been using the PyRosetta JobDistributor which should allow you to launch many instances of the same script in parallel, and each instance will work on a different decoy. Thus, for your N decoys each instance will work on approximately N/m of them, where m is the number of individual instances of the script you run. I have been running on our cluster, and noticed that after launching say a dozen instances of the script, after a number of minutes, some instances would start dying. After a few more minutes, I'd be down to only a few instances still running.

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PyRosetta - General

Having trouble producing a .pdb file from a silent output file after running abinitio relax

Submitted by burkheadlab on Wed, 2011-03-09 12:48

Well I have run AbinitioRelax.linuxgccrelease for the first time and had it produce a t000_silent.out file. The documentation says to use score.linuxgccrelease but that no longer exists in rosetta 3.2. What do I need to do to get .pdb files from the silent output file? Thanks.

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Rosetta 3 - General

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