The problem hasn't been solved
can AnchoredPDBcreator be used for inserting a helical anchor onto a surface helix?
Since, the results of Relax refinement doesn't make much differences.
Thank you very much!
Hi
I wonder if anyone has any ideas how I might do this. I have a protein where I know some of the surface exposed residues (from labelling experiments) and I was wondering if there was a way to use this as a constraint in structure production. For example is it possible to say that the amines (Nz) of lysines X,Y and Z must be solvent exposed?
Thanks for any suggestions you might have.
Best wishes
Chris
Hi, I am trying to learn Rosetta Scripts and need to see some examples. The link provided in manual: https://svn.rosettacommons.org/trac/browser/trunk/mini/demo/rosetta_scri... requires password. Anyone could help me with it?
Thank you very much!
Can the executables be run from command line like a command by just typing "executable-name" without "./executable". If so how? I have downloaded and installed rosetta3.3 in my home folder. My OS is Ubuntu 10.04.
Hello. I am quite new to Rosetta, Cygwin, Scons. I am currently running Windows 7 64-bit. I so far have installed MinGW, cygwin, python 2.7.2 and scons.
Here is the message I get from cygwin:
$ scons.bat bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "C:\users\jaewon\documents\source\rosetta\rosetta_source\SConstruct", line 139, in main
build = SConscript("tools/build/setup.py")
File "C:\Python27\Scripts\..\Lib\site-packages\scons-2.1.0\SCons\Script\SConscript.py", line 614, in __call__
return method(*args, **kw)
Greetings Rosetta Team,
Now that I've resolved my ligand_docking issues (big thanks to Rocco!) I would like to generate and screen symmetric protein+ligand homo-multimer structures.
First, in order to get SymDock to recognize my ligand and generate output, I had to rename one of the ligand's carbon atoms "CA".
Not a big deal, but it required changing the name for each occurrence of the ligand (input .pdb, parameter files, and rotamer libraries).
For the test case, SymDock.linuxgccrelease was run using PBS on four cores with the following flags:
Dear:
I would like to compile Rosetta with 'extras=mpi' option but failed. It always said the following:
sh: mpiCC: command not found
scons: *** [build/src/release/linux/2.6/64/x86/gcc/mpi/apps/public/AbinitioRelax.o] Error 127
I want to design the sequences of an enzyme. I am not sure which method should I use. I am thinking of 2 methods:
1. Use fixbb and fix the enzyme site of the protein. just design the other part of the protein
2. Use Enzyme Design of rosetta 3.3. But this program seems only design the active sites.
Do you have any ideas? Thank you very much!
Hi,
I use Rosett_3.3 to design a protein whose length is 166. And the command is
fixbb.linuxgccrelease -s protein.pdb -resfile protein.resfile -ex1 -ex2 -nstruct 1 -database $ROSETTA_DATABASE -jran 111111 -fast_sc_moves True
However, it takes me more than 2 hour to finish the job. I use rosetta 2.3 to design the same protein with the same parameter. It takes me only 1-2 minutes.
Could you please tell me what parameters should I use to make the program fast?
