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Can someone please give an example of a simple xml file and commandline for running the GreedyOptMutationMover to optimize the affinity of an interface of 2 proteins in a PDB file by mutation residues in a sequence of one of the proteins? The protein being mutated is relatively stable but the mutations are in a loop. What taskoperators and additional movers (repacking or backrub?) are necessary for doing this and reporting the change in ddG?
Hi, good day everyone,
I was trying to compile Rosetta 3 and after running smoothly for two hours it stopped, and I got the following error message:
g++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
scons: *** [build/src/release/linux/5.3/64/x86/gcc/7/default/core/io/pose_from_sfr/chirality_resolution.os] Error 4
Dear Sir or Madam,
previously I have always downloaded Rosetta with binaries. But for now the Rosetta package with binary files became too huge (over 17 GB), which makes the Rosetta package download through slow browser (1 Mbps in average and it doesn't depend on a browser) really complicated deal. Other problem, which complicates downloading the Rosetta package, consists in that, what the download process is aborted when laptop screen fades and laptop go to sleep mode.
Hello,i use scons to complie.
Recently,I write some class in .cc and .hh files , when i #include<~path/name.hh>,i find that it did not compile .cc files. I have read sconstruct file but do not know how to add my own file to compile with.
Please give me some help
I have recently downloaded and untar new version of Rosetta - as a rosetta_src_2020.03.61102_bundle folder. When I tried to compile it via standart command "./scons.py -j6 mode=release bin" in /main/source/ directory, I got such error:
"g++: warning: switch '-ffor-scope' is no longer supported
Undefined symbols for architecture x86_64:
"protocols::abinitio::ResolutionSwitcher::ResolutionSwitcher(core::pose::Pose const&, bool, bool, bool)", referenced from:
protocols::moves::MonteCarlo::boltzmann(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, double, double) in MonteCarlo.os
"vtable for protocols::abinitio::ResolutionSwitcher", referenced from:
Im not really sure how this all works so I'll just describe my phenomenon. Im running Ubuntu18.04. I switched using the conda installer to install the latest build of Pyrosetta4, but then I noticed I was missing some of the features which are pulled from Rosetta. The specific example I am working with is the ShapeComplimentarityCalculator example. When I install from the conda so that the latest Pyrosetta is running from :
I just set up everything in conda environment, and everything seems working great, except that I can't get pymol mover working - when I run PyMOLRosettaServer.py, I get:
PyMOL not running, entering library mode (experimental)
pyMOL <---> PyRosetta link started!
at 127.0.0.1 port 65000
despite that my pymol is running perfectly fine. What should I do to make pymol mover work? Any help would be very appreciated.