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Problem with SymmDock in helical symmetry

Submitted by mumdonar on Wed, 2013-09-18 03:59

Keywords:
SymmDock
Helical Symmetry

Dear RosettaCommons,

we're trying to model a protein complex in helical symmetry with SymmDock in Rosetta 3.5.
There is one problem occuring always, which we coundn't solve so far: In most of the resulting
models there are single residues displaced from the backbone of the protein. Often the whole structure
looks completely broken. Relating to this we made the observation that the master subunit is not affected
but the strength of the effect (number of displaced residues) increases with the number of jumps between the master

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Rosetta 3 - Applications

mutate residue at termini

Submitted by jarek on Fri, 2013-09-13 09:24

interface design is changing a terminal aminoacid in my complex and
I would like to mutate it back to wildtype using the MutateResidue
mover, but every time I try to do that for the N or C terminus I get
segmentation fault. This is system independant, I see this for every complex I work with.
Is there a way around it, without going back to the interface design ?

Thanks

Jarek

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Rosetta 3 - General

ddg calculation

Submitted by Lindsay on Thu, 2013-09-12 10:19

Hi,
I try to use Rosetta 3.4 to calculate the ddG of a protein.
The command I use is
$ROSETTA/rosetta_source/bin/ddg_monomer.linuxgccrelease -in:file:s test.pdb --ddg::weight_file ddg.wts -ddg::iterations 20 -ddg::dump_pdbs true -database $ROSETTA/rosetta_database/ -ddg::local_opt_only true -ddg::min_cst false -ddg::mean true -ddg::min false -ddg::sc_min_only true -in:file:fullatom -resfile test.resfile

Everything goes well but some proteins have problems.

For example core.pack.task.ResfileReader: On line 2, the pose does not have residue with chain=A, PDBnum=1

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Rosetta 3 - General

About scorefunction.

Submitted by Run on Mon, 2013-09-09 23:08

This is the result of abinitio.I found there are six kinds of scorefunction(score0,score1,score2,score3,score4,score5).I don't know the difference of them.Would you please tell me something about these six kinds of scorefunction?Thank you.

Stage 1
Folding with score0 for max of 2000
protocols.abinitio: Replaced extended chain after 15 cycles.
protocols.moves.MonteCarlo: ClassicFragmentM trials= 15; accepts= 0.9333; energy_drop/trial= 0.00000
protocols.abinitio: ------------------------------------------------------------
Scores Weight Raw Score Wghtd.Score

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Rosetta 3 - Applications

Available of some protocals mentioned in publications

Submitted by SunH on Mon, 2013-09-09 20:47

Hi all,
When the simulations protocol mentioned in "Large-scale characterization of peptide-MHC binding landscapes with structural simulations" will be released? The papers says the protocol will be available in next public release but I can't find it in Rosetta latest version 3.5.

Thanks

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Rosetta 3 - General

NaNs for the p_aa_pp Score Term

Submitted by protos_heis on Mon, 2013-09-09 06:23

I've been having a very strange issue with the energies of a PyRosetta script I have been working on. It seems that I am getting NaN returned as the score value as I make mutations to a pose and upon further inspection it seems that the source of the NaNs is the p_aa_pp term. Specifically it seems that the score function subroutine of "eval_ci_1b" is the one producing the NaNs and "eval_ci_2b" doesn't seem to produce NaNs at all.

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PyRosetta - Build/Install

Git branches for weekly releases

Submitted by stranges on Fri, 2013-09-06 15:25

Question about the weekly releases. Is there a way to get these using git?
The packaged downloads are great, but it would be more convenient if we could just get an update to save downloading a new source tree every week or so.
If this is possible could you outline how to do it, or point me in the direction of something that would help? I couldn't find anything in the software section that outlined this.
For those of us who would still like updates but are not in Commons labs at the moment this would be a big help.

Thanks in advance, I miss you guys.
Ben

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Rosetta 3 - Build/Install

How to get the GDT_TS?

Submitted by JadAbbass on Thu, 2013-09-05 11:59

Dear all,

I have got results (silent and score files)for many targets. Although, I provided the native file, I couldn't find the GDT_TS in the score file.

I have got the rmsd, but I need both rmsd and GDT_TS. Is there any Rosetta's tool (or even an independent tool) to calculate the GDT_TS of a native structure against a silent file?

Thank you in advance,
Jad

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