The problem has been solved
How do I add virtual atom to my cofactor (metal ion) in rosettadock? [Solved]
When I tries to use FlexPepDocking it bails out ERROR: total_residue() != 0. Though I have been able to use the same pdb file with the web server. It appears that FlexPepDocking generate a pose that do not contain any residues and that the assert statement in Pose.cc bails out due to this reason. Is there anything wrong with my pdb file, I have also tried to include a co-factor which is parameterized. This error appear but with and witouth any co-factor.
FlexPepDockingPoseMetrics: (1) Isc: -8.11514
FlexPepDockingPoseMetrics: (1) Total BSA is: 659.381
There are several reports of build failures with gcc 4.4 in these forums. I also had compile errors with gcc 4.4, but I have found a workaround (although I have yet to evaluate the impact of this workaround on performance)
Here is my situation:
- working on a cluster where I have little control on available compilers
- readily available compiler is gcc 4.4.2
- working with Rosetta 3.1
Compile results with "./scons.py -j8 bin extras=static" :
scons: done building targets.
no errors
310 warnings
The option setting is missing an entry for gcc 4.5. Please add 4.5 to the default options.setting.I have attach a options.settings. Please include me in credit.
Knut J
Hi All,
I would really like to generate a fragment library from a metal binding peptide primary sequence (as in the metalloprotein_abrelax demo). I would like to generate a fragment library from a sequence like:
>1dsvA.A
PPGLC[CYZ]PRC[CYZ]KKGYH[HIS_D]WKSEC[CYZ]KSKFDKDGNPLPPZ[ZN]
Possibly using chemical shift libraries as in Wang et al. (Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science).
Thanks! and all the best,
--Buz
The purpose of this topic is to collect holes in the 3.2 documentation. If you post a question here (and you may), please also echo it as its own thread, and look for answers there. I will collect questions from other topics into this topic, but I won't be answering here. Once we get our next major documentation drive going, we'll try to get all the documentation flaws exposed here patched. Feel free to post any issues with the documentation you know about; the more specific the issue the more likely we can fix it. Thanks.
Hi Everyone!
The Beta version of PyRosetta 2.0 is ready for download, here is a brief summary of changes:
Approximately 4x more C++ namespace are bound.
All classes now have proper base classes.
Various usability improvements: better help, better error detection, etc.
Build system has been completely reworked. Supports parallel builds. Beta support for Clang++.
Build bases on Rosetta 3.2 release code (also available soon!).
Binaries for the following platforms are ready for download:
Mac OS X 10.6 (64Bit)
Scientific Linux (64Bit)
ERROR: Unable to open weights. Neither ./interchain_cen nor interchain_cen.wts nor ./scoring/weights/interchain_cen.wts exist
ERROR:: Exit from: src/core/scoring/ScoreFunctionFactory.cc line: 177
WhenI type:[root@localhost rosetta_source]# python external/scons-local/scons.py
This happens:scons: Reading SConscript files ...
sh: svnversion: command not found
sh: svn: command not found
scons: done reading SConscript files.
scons: Building targets ...
o build/src/debug/linux/2.6/64/x86/gcc/numeric/constants.os -c -std=c++98 -pipe
-ffor-scope -W -Wall -pedantic -Wno-long-long -O0 -g -ggdb -ffloat-store -fPIC -
Isrc -Iexternal/include -Isrc/platform/linux/64/gcc -Isrc/platform/linux/64 -Isr
Hi all,
I was wondering if there were any plans to add RosettaMatch to the Rosetta 3.2 distribution?