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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

Duplicated Magic Number

Submitted by jurkm on Thu, 2011-11-03 11:26

Hello,

I modified an existing mover. Compilation finishes without any problems. When starting Rosetta I get the following error:

../rosetta_source/bin/minirosetta.macosgccrelease @flags
Duplicate magic number in random object initialization! Number:84195
ERROR:: Exit from: src/numeric/random/random.cc line: 136

It seems basically all movers initialize their own RandomnumberGenerator with different seeds. So why is Rosetta complaining in this particular case and not with the other movers? What have I missed?

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Rosetta 3 - Build/Install

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