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questions about ab init membrane protein

I am trying to use the membrane ab initio modeling application by the following command: (fasta file) (span file) (path to blastpgp) (path to nr database) (path to script)

    example: (path to mini)/mini/src/apps/public/membrane_abinitio/ BRD4.fasta BRD4.span /work/bjornw/Apps/blast/bin/blastpgp /scratch/shared/genomes/nr ~bjornw/mini/src/apps/public/membrane_abinitio/

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Installation of rosetta 3.2 of fedore core 6 platform

Hi ,

I am trying to install rosetta 3.2 on fedore coer 6 platform but I am getting the following errors after giving scons bin mode=release command :-

[root@bmel rosetta_source]# scons bin mode=release
scons: Reading SConscript files ...
svn: '.' is not a working copy

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/usr/local/rosetta-3.2/rosetta_source/SConscript", line 40, in

scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.

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Performance improvement in AbinitioRelax and relax 3.2 ???

I got the following benchmarks for AbinitioRelax and relax (version 3.2). The speed improvement I observed compared to 3.1 are so important that I am wondering if they are real. I would appreciate if someone could confirm that such improvement (3.2 vs 3.1) is really to be expected.

System : 90 residues protein

Protocols tested :

1. "AbinitioRelax -abinitio -out:nstruct 100"
2. "relax -relax" (3.1) or "relax -relax:thorough" (3.2) on above abinitio structures
3. "relax -relax:fast" on above abinitio structures

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NMR / NOE related tools in 3.2 ?

Is there an increase in NMR functionality in 3.2? Although I saw nothing in the 3.2 documentation to suggest this, the 3.2 version of "relax -help" and "score_jd2 -help" now suggests a wide array of NMR-related options (see attachment with partial output from "relax -help". So, are there really new NMR-related tools in 3.2? Are those documented somewhere?


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installation of rosetta 3.2 on windows 7 home edition using cygwin 6.1 (intel i5 )

Hi I tried installing rosetta 3.2 on windows using cygwin and I have installed zlib while installing cygwin but I am getting the following error :-

End of stack trace
12353592 [main] python 5504 fork: child 3364 - died waiting for dll loading, err
no 11
scons: *** [build/src/release/cygwin/1.7/32/x86/gcc/utility.dll] Resource tempor
arily unavailable
scons: building terminated because of errors.

What could have gone wrong ??

I again tried using the same command and I got the following error :

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Peptide design


I would like to perform sequence design of the peptide bound to the protein. I am using PyRosetta and PackRotamersMover function. I would like to ask if it is possible to use BINDING ENERGY of peptide instead of TOTAL ENERGY of complex as a criterion for accepting/rejecting given mutation during Monte Carlo simulation?


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Re : installation of rosetta 3.0 on fedora core 6


I am new to rosetta .. I have downloaded and installed rosetta 3.0 on fedora core 6 platform .. I gave the commnand scons bin mode=release, being in the rosetta3_source directory.. as it was complied wihtout any errors.. but i don't know how to use it for any procedure .. after checking the manual .. I followed some steps and being in the loopmodeling directory rosetta3_demos I gave the following command :-

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I'm a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =)

Hi, I'm currently an undergraduate research student in Singapore. My prof has just tasked me to try out Rosetta for docking. However, he is also new to the program, and so we are sort of stuck on how to start even a basic docking. We are using SUSE Linux. We hope that someone would be kind enough to get us started on a very basic tutorial on docking like the commands used, before we proceed on to explore the features further.

Thanks. =)

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