The problem has been solved
At RosettaCON2011, many of the developers and users got together to write documentation for an afternoon under the beautiful, central Washington sunshine. I've put up a beta release of the tutorials that we assembled at RosettaCON2011 at
http://rosettadesign.med.unc.edu/collaborators/RosettaCon2011/RosettaCON....
I downloaded Rosetta3.3_bundles.tgz, but file failed to be uncompressed. I downloaded rosetta3.3_source.tgz and rosetta3.3_database.tgz packages and tried to install it on my Fedora 13, which supported Rosetta 3.1, 3.2 and 3.2.1. Unfortunately, the compilation of Rosetta 3.3 failed by Segmentation fault. My system uses scons-2.0.1-1.fc13.noarch. I used "scons bin mode=release" command line.
The second question concerning the new release is: apart from the new functions, is there any change/improvement on the old programs (for example AbinitioRelax) exist in release 3.2.1?
I would like to use a specific library for design using new distributions of P (Res | phi, psi). I found 7 files in the rosetta_database directory that seem to be exactly what I'm looking for: Paa, P_AA, Paa_n, P_AA_n, Paa_pp, P_AA_pp, P_AA_pp_08.2009
Our lab is in the process of becoming a Rosetta developer officially once again, but that will take some time.
First, can anyone point me in the right direction as to the format of each of these files/how each of them are used?. Some, like P_AA seem fairly obvious, but some of the others I have no idea.
Hi!
How can I read parameters of several metal ions, solvent molecules or ligands?
When I try to run this:
from rosetta import *
init()
params_list=Vector1(['SO4.params','K.params','MG.params'])
res_set = generate_nonstandard_residue_set(params_list)
I get the following error:
...
In [4]: res_set = generate_nonstandard_residue_set(params_list)
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types
ERROR: Residue names must be unique!
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 358
Charmm29 (I don't know about more recent versions) labels many hydrogen atoms as HB1, HB2 etc. Rosetta however, looks for 1HB, 2HB etc. For most residues this causes no problems even though Rosetta can't identify the hydrogens, however, a problem arises in the case of proline, as Rosetta misidentifies such residues as hydroxyproline. A simple fix is to massage a pdb derived from Charmm with the following awk script before reading it into Rosetta. The script also changes HSD and HSE to HIS and fixes an ILE atom name.
# This file is fixcharmm.awk and runs under linux.
I would like to try and build PyRosetta from source to get it working on our shared cluster. With 1.1 it was readily available, but how do I obtain it for 2.0?
-Jared
I am trying to build Rosetta 3.2.1 on Fedora14.
I have scons v2.0.1, Python 2.7, gcc 4.5.1
Everything seems to go fine, and then after about 20 minutes I get this:
scons: done reading SConscript files.
scons: Building targets ...
scons: `bin' is up to date.
scons: *** Do not know how to make File target `cxx' (/home/jarek/packages/Rosetta/Rosetta-3.2.1/rosetta_source/cxx). Stop.
scons: building terminated because of errors.
Any ideas how to fix this?
Thanks !
Jarek
Hi,
I'm quite new to rosetta design i'm trying to understand all the possible options to design a DNA-protein interface.
I was using rosetta_source/test/integration/dna_interface_design/design.script but I have a couples of questions on the output:
what is a "MultiState Fitness" could please give me an idea of the range of this value?
which is the difference between "SeqScore(binding)" and "SeqScore(bound)"?
which is the difference between "Specificity(binding)" and "Specificity(bound)"?
So I've run abinitiorelax for a protein and I now have a large number of good structures that I have extracted to *.pdb files. I have run this cluster command on them as well...cluster.linuxgccrelease -database /opt/rosetta-3.2.1/rosetta_database/ -in:file:s *.pdb -in:file:fullatom -cluster:radius -1
Is this a good way to cluster or is there a better way to do this?
Hello,
Is it true that there is a maximum number of lines with constraints in the external file that Rosetta can process? This should be around 490.
I played around with constraint files (trying to reproduce my last error (http://www.rosettacommons.org/content/using-degenerate-protons-rosetta3x) and what I realized was, that Rosetta does read the following file without problems: