Symmetric abrelax modeling
Submitted by SenyorDrew on Fri, 2011-02-18 10:14
Is it possible to use the symmetry code to fold something like an Ankyrin repeat?
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sam.predict-2nd for make_fragments.pl script
Submitted by sumukh21 on Thu, 2011-02-17 12:29
Hi
Could anyone tell me where to get predict-2nd software for membrane_abinitio application ? I am trying to run make_fragments.pl and it is asking for predict-2nd software. Could anyone please help me ?
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error while building rosetta++
Submitted by asmi on Thu, 2011-02-17 11:26
Hello
I am new to rosetta. When i am trying to build rosetta by typing make gcc,i am getting a long message a part of which looks like this:
src/utility/io/zipstream.ipp:657: instantiated from ‘void zlib_stream::basic_zip_ostream::add_footer() [with Elem = char, Tr = std::char_traits, ElemA = std::allocator, ByteT = unsigned char, ByteAT = std::allocator]’
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Username and Password for download link?
Submitted by juden99 on Thu, 2011-02-17 03:30
Hello,
I applied for the express academic license for pyrosetta and received the license email very rapidly. However, as compared to the Rosetta license where I also received an email with the download link and username and password, I did not receive such for Pyrosetta. Any ideas?
Thanks so much,
Judy
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excecutable files don't work -- Rosetta3.2 on WindowsXP
Submitted by mn on Wed, 2011-02-16 01:10
Hi
I tried installing rosetta 3.2 on windows XP using cygwin1.7, gcc 3.4.4. following a procedure posted on 10/20/2009.
It seems I was able to compile rosetta3.2. There are "executable files" in rosetta_source/bin folder and rosetta_source/build/src/release/cygwin/1.7/32/x86/gcc folder. They look like AbinitioRelax.cygwingccrelease, backrub.cygwingccrelease and so on.
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Fragment files for membrane_abinitio application
Submitted by sumukh21 on Tue, 2011-02-15 17:23
Hi
I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta
The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.
Could anyone please help in this matter ?
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How to estimate the effect of a mutation on the binding energy?
Submitted by ltrabuco on Tue, 2011-02-15 08:02
Given a protein complex, I would like to estimate the effect of a point mutation on the binding energy (ddG). I'd appreciate if anyone could point me to the Rosetta app(s) that I should look into. I'm fairly new to Rosetta.
Thanks!
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how to relax structure constraining CA in Rosetta3.2?
Submitted by albumns on Tue, 2011-02-15 06:15
Hi
I am wondering how to relax structure constraining CA in Rosetta3.2?
I found that each protocol contains two executable command such as:
relax.default.linuxgccrelease relax.linuxgccrelease
is there any differences between these two?
THX
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Fragment files for membrane_abinitio application
Submitted by sumukh21 on Sun, 2011-02-13 20:34
Hi
I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta
The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.
Could anyone please help in this matter ?
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is it possible to ab initio only a part of a protein?
Submitted by albumns on Sun, 2011-02-13 08:10
I've built a homology model but a part of it (around 12aa)is not reliable because there is no homology template in this region. The whole protein is around 350aa. And I am wondering is it possible built a ab init model based on my initial model to complete these unreliable region?
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