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Rosetta ab initio with disordered regions

Submitted by smiruthi on Thu, 2011-12-15 14:37

I don't have experimental data on the disordered region of a protein and tried different online prediction servers and obtained contradictory results. Disopred2 was used in the Wang et al PLoS 2011 rosetta paper but I am not sure about the accuracy. I was wondering if there were any suggestions on how to proceed?

Thanks a priori.

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Rosetta 3 - General

ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'

Submitted by smiruthi on Mon, 2011-12-12 14:27

I get this error when I try to combine my silent files (using Wang et al Disorder predictions with REPLONLY residues:

core.io.silent: Finished reading 2744 structures from silent_1270984.mgt.out

ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.hh line: 151

Thanks a lot a priori.

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Rosetta 3 - Applications

No read_resfile routine?

Submitted by gjbartlett on Mon, 2011-11-28 08:45

Hello,

I've been trying to run the Packing and Design tutorial with a view to writing my own Packing/Design routine. I'm following the pdf posted on the PyRosetta website and the errata page. There doesn't appear to be a read_resfile routine for either standard_packer_task (as per the original instructions) or create_packer_task (listed in the errata).

I get "AttributeError: 'PackerTask_' object has no attribute 'read_resfile'"

I'm running the latest Windows native build PyRosetta build. Any help gratefully appreciated.

Many thanks,

Gail

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PyRosetta - Scripts

limit_cluster_size default value

Submitted by sacch on Thu, 2011-11-24 17:57

Dear all,

I looked into the source code of Rosetta and found out that if in the input we don't assign -cluster:limit_cluster_size (default is -1), it seems the cluster size will be zero (line487~499, protocol/cluster/cluster.cc)? Could someone please explain what is going on here?

in line 495, there is screening of j<=limit, which means, if limit is negative, the cluster list will never be populated. The weird part is that I still get good clusters if I don't give this value in the input.

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Bug in cluster?

Submitted by nitroamos on Mon, 2011-11-21 12:53

When I run the cluster application with the following command:

cluster.linuxgccrelease -database ~/rosetta3.3//rosetta_database -in:file:s *.pdb -in:file:fullatom -cluster:radius -1 -cluster:gdtmm -cluster:limit_clusters 25 -cluster:limit_total_structures 100 -cluster:sort_groups_by_energy

I'm getting lines with:

protocols.cluster: Adding struc: 2.32622e-310

in the output... There's nothing suspicious about the rest of the output, and it seems to be giving me reasonable results...

Is this a bug, or am I doing something wrong?

thanks!

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Rosetta 3 - General

PyRosetta version 2.011 for Mac/Linux is ready to download!

Submitted by Sergey on Mon, 2011-11-21 08:51

Hi Everyone,

PyRosetta version 2.011 for Mac/Linux is ready to download!

Release notes:
- PyRosetta - PyMOL integration.
- All Rosetta classes can be subclassed in PyRosetta.
- It’s now possible to define custom energy terms in PyRosetta (Examples can be found in test/*Subclassing*)
- Rosetta libraries updated to r45995 (Nov 2011)

For download links for various distribution visit: http://www.pyrosetta.org/

Sergey.

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Rosetta3 Tutorials

Submitted by smlewis on Fri, 2011-11-18 07:33
Category: 
Structure prediction

At RosettaCON2011, many of the developers and users got together to write documentation for an afternoon under the beautiful, central Washington sunshine. These tutorials will be officially released shortly (at the same download location as Rosetta, http://www.rosettacommons.org/software/).

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Rosetta 3 - General

Rosetta releases and revision numbers

Submitted by ShaneOConnor on Thu, 2011-11-17 13:55

Hi mini,

It's happened to me a few times that I've needed to check out older versions of Rosetta for compilation. Sometimes it's also handy to know the revision numbers of the releases quickly. I've not yet found a list of releases and their SVN revision numbers so I created the following. Please correct it if I've made any mistakes. To add to Rocco's comment below, please note that the corresponding trunk revisions are approximate i.e. tThey correspond to the point of branching from the trunk but the releases may include bugfixes from later trunk revisions.

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