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loop modeling during enzyme design?

Submitted by lzx32 on Wed, 2011-11-16 00:30

Dear developers:

I noticed that some loop modeling options (e.g. kic_looop_sampling) are now included for the enzyme_design.linuxgccrelease protocol in Rosetta3.3.

It seems that the capacity to remodel loops in the substrate-binding pocket will significantly improve the enzyme_design protocol. But since this has not been mentioned in any papers or tutorials, are the loop modeling options fully working now, or are they still under development?

Thanks for reading...

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Rosetta 3 - Applications

fragment_picker with fasta only

Submitted by gw on Tue, 2011-11-15 13:20

I would like to generate a fragment library based on a sequence. I tried running the fragment_picker demos in rosetta3.3/rosetta_demos/fragment_picker and it seems I need to include a pdb and also psipred (.ss2) file. The documentation seems to say that only vall .fasta .wghts are mandatory. I only have sequence -- can I still run this protocol?
http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_...

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Rosetta 3 - Applications

ERROR: unrecognized atomtype property VIRTUAL

Submitted by harshkhare on Mon, 2011-11-14 09:40

Hello,
I have built Rosetta3.3 using gcc-4.3 which went smoothly without errors. While running any rosetta script(xml file) using rosetta_scripts.linuxgccrelease, i am getting the error 'unrecognized atomtype property VIRTUAL'. When the same script is run using rosetta_scripts.linuxgccdebug, the error doesn't occur. Please suggest me the solution for this error. Following is the error i am getting.
##BEGIN ERROR MSG##

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

ERROR: unrecognized atomtype property VIRTUAL
ERROR:: Exit from: src/core/chemical/AtomType.cc line: 108

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Rosetta 3 - General

Can not build the parallel version of rosetta-2.3.1 (the SnugDock). Help!!

Submitted by ice_flame on Fri, 2011-11-11 07:47

Hi all,

I was trying to build a parallel version of Rosetta-2.3.1(SnugDock) on my workstation. My OS is RHEL 5.4(32-bit), and I use Openmpi-1.4.3.

I tried to compile it as I did to Rosetta2.3.0 on the same computer and the very same OS and MPI compilier, but it didn't work.

I got the following errors:

######################
job_distributor.cc:(.text+0x5ada): undefined reference to `pathways::pathways_generator_main(bool&)'
collect2: ld return 1
make: *** [rosetta.mpilam] error 1

######################

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Rosetta++ - Build/Install

Calling A Protocol From Another Protocol

Submitted by jurkm on Wed, 2011-11-09 09:50

Hi,

I am having trouble calling other movers from the protocol I created and cannot find a solution. Maybe it is obvious again, but I cannot see it.

I modified the minirosetta routine to call my protocol (SymEns), which looks like the following code. This works fine and indeed generates useful output.


int
symens_main()
{
SymEnsProtocolOP assembly_mover = new SymEnsProtocol;
protocols::moves::symmetry::SetupForSymmetryMoverOP setup_mover = new protocols::moves::symmetry::SetupForSymmetryMover;

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Rosetta 3 - Build/Install

Windows 7 64 bit OS using Cygwin build error?

Submitted by Mdlane on Mon, 2011-11-07 08:31

Hi all, new poster, new to Rosetta.

I've been trying to get Rosetta to run on a Windows 7 64 bit OS using Cygwin. I thought I had finally made progress when I got the build to successfully complete (my Bin and Build directories were populated, as expected), but whenever I try to run any program from my Bin folder (I'm focusing on docking programs), it gives me an error:

"error while loading shared libraries: protocols.dll: cannot open shared object file: No such file or directory"

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Rosetta 3 - Build/Install

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