The problem hasn't been solved
Hi,
How should I site the scoring application of rosetta3.1 in an article?
Thank you,
Doran
symmetric docking uses the minimal subsystem during docking. The output contains also the smallest subsystem. For example, in a C17 system (3kml), only three neighboring subunits are used in docking and the output decoys contain also only three subunits (DiMaio2011, PLoS ONE). How to reconstruct the complete system based on the output? It seems the original symmetric definition file can not be relied on any more.
It seems that both relax and backrub do localiezd sampling using the Metropolis criterion. Could any one tell me the differences between them? Thank you very much!
In looking to try out a build of Rosetta so that a researcher in another
department can try it out on a large memory resource we have here, I
noticed, because I ended up looking at this file, that there's a stanza
in
tools/build/basic.settings
that appears to allow for compilation against a CUDA toolkit.
As I am not a Rosetta user but an implementer, I was wondering if there's
a simple test/demo that I could try out, if I build such a variant, which
would be an Ubuntu 10.10 (GCC 445) with NVIDIA_GPU_Computing_SDK-4.0.
I logged in as a regular user without superuser privilege.
After I downloaded rosetta 3.4, and unzipped the file "rosetta3.4_bundles.tgz", I unzipped all the .tgz files in the directory "rosetta3.4". In the sub-directory "rosetta_source", I typed "python external/scons-local/scons.py bin mode=release". After some time (hours), the compilation seems completed. then in the directory rosetta3.4/rosetta_source/bin, I typed "minirosetta.linuxgccrelease", get the following error message:
core.init: Mini-Rosetta version unknown from unknown
core.init: command: minirosetta.linuxgccrelease
According to the instruction, I first installed scons and tested it, it seems working:
*********************
~/scons-2.1.0$ scons --version
SCons by Steven Knight et al.:
script: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine: v2.1.0.r5357[MODIFIED], 2011/09/09 21:31:03, by bdeegan
on ubuntu
engine path: ['/usr/local/lib/scons-2.1.0/SCons']
Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009,
2010,
2011 The SCons Foundation
**************************
Then I run Resetta installation and get error below:
When predicting ddg, I find that the ddg has physical unit. But the score of design doesn't. How to transfer the energy score to real physical unit? Thank you.
I could not find instructions on PyRosetta site or this forum on how to read in a silent file so I can obtain a set of poses at once. It is not in the FAQ, either. Or should I always extract_PDBs from the silent file first ?
Dear Rosetta developers,
I am interested in the de novol design of a peptide with helical conformation which could bind a specific protein partner with enhanced affinity. However, when consulting the user guide, i lost my way about the specific method. So could you be so kindly to tell me which method or module in Rosetta can do such kind of case , or provide me a step-by-step guidance.
What i intended to do was listed in the following:
Can one consider prepack before docking as a fast relax of subunits with backbone constraints?
If so, can one replace prepack step with a fast relax with backbone constraints of subunits?
