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some "COMMAND ERROR" while installing rosetta2.1.0

Submitted by sdg_lab on Wed, 2012-03-21 22:57

I am trying to install Rosetta++2.1.0
and I changed the options.settings file to be compatible with gccc 4.5 which is in my my CYGWIN
but I am getting the following big error.

I will be very grateful if somebody could suggest a solution:

ERROR :
cygwin warning:
MS-DOS style path detected: C:\Documents and Settings\All Users\Application Da ta\scons/site_scons

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Rosetta++ - Build/Install

Does comparative modeling works for membrane proteins

Submitted by justin on Wed, 2012-03-21 04:58

Dear all,

Does comparative modeling works for membrane proteins?
I found a application called "topology broker" in the documentation on "TopologyBroker_GPCR" included in "protocol_capture-3.3" bundle. According to the abstract, this protocol has been used for modeling of metabotropic glutamate receptor subtype 5 protein using GPRC crystal structures. But the "flags" is only for rebuilding loops of a membrane protein whose crystal structure is known.

Does anyone know exactly how to use this?

Thanks!
-Justin Zhang

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Rosetta 3 - General

error running folding script on windows

Submitted by oppopomoz on Sun, 2012-03-18 15:56

when i run the sample folding script you can find on www.pyrosetta.org/scripts i get this error:

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PyRosetta - Scripts

Bug with make_pose_from_sequence when incorporating non-standard ResidueTypes in PyRosetta

Submitted by twc254 on Sun, 2012-03-18 12:27

I've been trying to assemble a poly-peptoid sequence using the make_pose_from_sequence function, however there seems to be an error in the way the polymer gets connected in the pose. For instance, the command:

make_pose_from_sequence(pose, "AAX[P02]AA", "fa_standard")

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PyRosetta - Scripts

error running the sample forlding script

Submitted by oppopomoz on Sat, 2012-03-17 06:15

when i run the sample folding script you can find on www.pyrosetta.org/scripts i get this error: init() got unexpected keyword argument 'keep_history' does anybody have any ideas about how to solve it?

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PyRosetta - Scripts

Residue_energy_breakdown utility

Submitted by cn on Sat, 2012-03-17 06:11

Hello,
I am planning to analyze residue interactions using residue_energy_breakdown utility as written in the documentation. However I could not find "residue_energy_breakdown" command in rosetta_source/bin.

I've built Rosetta3.3 in RedHat 5.4 by "scons bin mode=release" and build seemed to be finished without any problem.
Should I do any other things to use residue_energy_breakdown?

Thank you,

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Rosetta 3 - Applications

docking in rosetta 3.3

Submitted by Ammu on Thu, 2012-03-15 12:03

hi.................
i am new to rosetta. I have installed rosetta 3.3 in ubuntu linux 10.10. I wanted to do protein-protein docking & protein-peptide docking. so, can u help me to do this things. i have read the manuals of rosetta3.3 but i m unable to understand it correctly.Can you show me some direction to do this things & also how to create input files .pdb with only atom details for docking n other things also.............

thank you.....................

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Rosetta 3 - Applications