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Surface accessible residue as a constraint.

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

Post Situation: 

Rosetta 3.3 Compilation error

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)

Post Situation: 

Symmetry Docking and Clustering with Ligands

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:

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redesign a enzyme by fixing the active site

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!

Post Situation: 

Fix back bone design fixbb

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?

Post Situation: 

getting Rosetta to work with Phenix

I am trying to get Rosetta to work with Phenix phenix-1.7.3-928. But first I need to
get rosetta compiled. It does not compile without an error.I start with:

[rosetta@paprika ~/Desktop]$ python -V
Python 2.6.6

python scons.py bin mode=release

and it runs for a while and then:

Post Situation: 

is it possible to generate models without hydrogen?

I am using the kinetic loop refinement protocol these days. Since my protein is large than 300aa and the loop is over 20 aa. So it is really time comsuming even I use 24 CPU to run the jobs. It only generate 1 model after one hour.... I am planning to generate 5000 loop models. Is it possible to generate the loop model with hydrogen? At least without hydrogen for the no loop region?

THX

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