protein-protein docking with flexible backbone
Submitted by tim on Fri, 2013-12-20 05:52
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Ab-initio modeling on part of the protein
Submitted by xiayanlawrence on Thu, 2013-12-19 07:45
Hi all,
I have a design in which I replaced the sequence of the N-terminus region of protein A with the sequence of protein B, and got the chimera c. Now I would like to use Ab-initio modeling to simulate the possible conformations this protein B portion might adopt in the chimera, and I only want to carry out the simulation on this protein B region, while keeping the rest of the chimera structure fixed.
I would like to know what is the acceptable way of doing Ab-initio on only part of the protein?
Thanks so much for your help!
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fix backbone design of interface residue
Submitted by Lindsay on Tue, 2013-12-17 19:23
Dear all,
I am using rosetta3.5 to design the dimer interface of a known complex. I have designed hundreds of sequences but it seems that they are same. I use rosetta_source/bin/fixbb.linuxgccrelease @flag
the flag I use is
-s dimer.pdb
-resfile dimer.resfile
-database Rosetta3.5/rosetta_database/
-ex1
-ex2
-nstruct 10
-linmem_ig 10
-extrachi_cutoff 0
-ignore_unrecognized_res
-no_optH false
-skip_set_reasonable_fold_tree
-no_his_his_pairE
-mute core.io core.scoring core.conformation
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Rosetta 3.5 on Mac osx 10.9
Submitted by Atropian on Mon, 2013-12-16 22:10
Firstly let me start by saying that I'm fairly new to Linux, so go easy on the explanations...
I've installed scons and tried to unpack Rosetta but I keep getting the same error:
scons: Reading SConscript files ...
svn_version.py reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets ...
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minirosetta segmentation fault
Submitted by sabine on Wed, 2013-12-11 13:08
Hi,
I'm trying to run minirosetta, and i'm getting a segmentation fault without any further output. I'm attaching my input files, could you please help? (I can't attach the fragment files, they are too big.)
Thanks,
Sabine
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building rosetta 3.5 week49 on mac 10.9; hung up on testing
Submitted by bmooers on Wed, 2013-12-11 12:24
I am trying to build, install, and test rosetta weekly build 49
on a MacBook Pro running Mac OSX 10.9. I had upgraded from
10.6.8 and thought I had worked out all of the issues. My default
python is the Apple version.
Python 2.7.5 (default, Aug 25 2013, 00:04:04)
[GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
I reinstalled git but I still get a FATAL ERROR message about some issue
with git or the Conscript file.
Running versioning script ... fatal: ambiguous argument 'HEAD': unknown revision or path not in the working tree.
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Link to weekly releases?
Submitted by fukamitka on Tue, 2013-12-10 18:53
Where can I find a link to the latest weekly release?
https://www.rosettacommons.org/node/3409
> Latest weekly release: 2013wk48 (3-Dec-2013; academic license).
> Now available in the Software page.
It should be in the Software page according to the news above,
though I can see only links to version 3.5 or older in the download page.
Is it only for academic person, not for commercail licensee?
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Protein folding using Monte Carlo derived techniques and implicit solvation
Submitted by hefeweizen on Tue, 2013-12-10 06:30
I am looking for publications where Rosetta has been used to successfully fold proteins from sequence and where implicit solvation model has been necessary, could you give me some references?
Thanks
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scoring models
Submitted by peony on Fri, 2013-12-06 02:45
I've got two models of protein predicted from contact map. Using the energy terms what can I say about them? Can I see that they are bad? Or that they are for example mirror-images?
Results for model 70 :
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ligand docking, how to combine some silent.out files into a silent_all.out file
Submitted by Ryhon Wang on Fri, 2013-12-06 01:53