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Cluster gdtmm vs. rmsd

Submitted by brspurri on Thu, 2012-04-19 08:19

Hi there,

I've been trying to find the definition of the cluster application's -gdtmm flag, and why we might use it over clustering by rmsd (no flag required).
All the examples I've run across use the -gdtmm flag, but again, I'm just not how exactly this is clustering.

Then, following that, when the flag -cluster:sort_groups_by_energy is used, how does it sort them? Does it label the first cluster as the one with the lowest average energy for all the structures in the cluster? It almost seems at odds with clustering by RMSD.

Any ideas?

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Rosetta 3 - General

analysis of clustering

Submitted by loris.moretti on Thu, 2012-04-19 02:52

Dear All,

I'm a new user of Rosetta software and I believe I have the usual questions to ask, but as long as I've searched (manuals and web) I couldn't find satisfying answers.
I have generated 30000 structures with the abInitio protocol in parallel, 100 structures each run taking care of the seed number. Afterwards I've combined the 300 silent outputs with the combine protocol.
then I've clustered all these decoys with the cluster protocol. The results after the clustering were 150 pdbs called c.*.0.pdb which I understood as the best scored structure from each cluster.

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Rosetta 3 - Applications

Rosetta 3.4 build error with

Submitted by aork on Tue, 2012-04-17 16:11

I've been trying to build Rosetta 3.4 on Ubuntu 10.04. I've tried compiling with both gcc 4.4.3 and 4.3.4. Both give me the following error:

src/protocols/canonical_sampling/ParallelTempering.cc: In member function 'virtual void protocols::canonical_sampling::ParallelTempering::finalize_simulation(core::pose::Pose&, const protocols::canonical_sampling::MetropolisHastingsMover&)':
src/protocols/canonical_sampling/ParallelTempering.cc:193: error: size of array 'exchange_accepts_' has non-integral type 'std::pair'

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Rosetta 3 - Build/Install

error with fragment_picker.linuxgccrelease

Submitted by jiongzhang on Tue, 2012-04-17 09:07

I got the error message when I run fragment_picker:
rosetta_source/bin/fragment_picker.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

I think this is because some part of the software didn't compile right, but I don't know where. Could anyone help me with this?
Thank you very much!

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Rosetta 3 - Applications

Possible documentation error

Submitted by imurch on Tue, 2012-04-17 00:11

Hi,

I just wanted to report what I think is an error in the documentation for versions 3.3 & 3.4.

On the "Using Constraints Files in Rosetta" page, in the function definition for a SPLINE function, the documentation currently says:
"SPLINE: histogram_file_path experimental_value weight bin_size ... If using RosettaEPR knowledge-based potential, replace with EPR_DISTANCE"

According to my reading of the source code (and my experience using it!) there is a field missing in that description. It should read something like:

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Rosetta 3 - General

Energy and RG in the new rosetta3.4 ( like RG_Energy.cc and RG_Energy_Fast.cc )

Submitted by sdg_lab on Thu, 2012-04-12 08:49

Hello

I have a huge database of PDB files and I need to calculate their RG along with their energy(any relevant scoring).
Earlier version of Rosetta had RG_Energy.cc and RG_Energy_Fast.cc type of files which did this kind of job.

Is there something similar for Rosetta3.4 ?
Please advise

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Rosetta 3 - General

symmetric Docking- TRIMER in Rosetta 3.4 ?

Submitted by sdg_lab on Thu, 2012-04-12 04:22

I need to do certain symmetric docking to generate its homodimer and homotrimer and I am using Rosetta 3.4 Symmetric docking to achieve it.

I used the following command to generate homodimers :

./bin/SymDock.linuxgccrelease -docking:dock_ppk -symmetry:symmetry_definition ./sym_def_dimer.dat -symmetry:initialize_rigid_
body_dofs -database ../rosetta_database/ -out:nstruct 2 -out:file:fullatom -s S_00000001.pdb

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