You are here

Unsolved

The problem hasn't been solved

double mutations scan

Dear ALL,
I try to scan all the possible double mutations use this command"~/rosettabin/pmut_scan_parallel.macosgccrelease -database ~/rosettadb -s 1ABC.pdb.gz -double_mutant_scan -output_mutant_structures -ex1 -ex2 -extrachi_cutoff 1 -use_input_sc
-ignore_unrecognized_res -no_his_his_pairE -multi_cool_annealer 10 -mute basic core".
But I also want to fix all the residues as NATRO except the mutated residues. What command should I use? Thank you!

Post Situation: 

Picking the correct model from a large set of decoys (30,000+)

Hi everybody,

I'm been fairly successful at creating a large list of decoys for several of my project (de novo, loop modeling, etc). My runs typically produce 30,000 to 50,000 decoy structures, which I am under the impression is a decent number.

What is the best method to determining the "most accurate" structure from these decoys? Do I cluster first, take the lowest energy (c.0.0.pdb). Or do I look at the top scoring structures from each cluster? (c.0.0.pdb, c.1.0.pdb, etc). Or do I score the entire set and take the lowest scoring structure to be the most accurate, without clustering?

Post Situation: 

Simple FoldTree Question

Hopefully a fairly simple foldtree problem:

I have a two chain protein complex where the end of the floppy tail of domain B also happens to be the root of domain B.
Since the interaction with domain A is significant I'd like to re-root and sample according to something like:

From:
FOLD_TREE EDGE 1 645 -1 EDGE 1 646 1 EDGE 646 1500 -1

To:
FOLD_TREE EDGE 1 645 -1 EDGE 1 646 1 EDGE 1400 646 -1 EDGE 1400 1500 -1

So I use:

ft = FoldTree()
ft.add_edge(1,645,-1);
ft.add_edge(1,646,1);
ft.add_edge(1400,646,-1);
ft.add_edge(1400,1500,-1);
ft.reorder(1400);

Post Situation: 

how to change the parameter weight in rosetta 2.3

Dear ALL,
I want to change the energy weights of rosetta2.3. It is easy to change weight in rosetta 3. I can find a weight file call "score12_full.wts“ in rosetta 3's database. But I can't locate the same file in rosetta 2.3. Where can I find the rosetta 2.3 energy weight file? Thank you!

Post Situation: 

Rosetta 3.4 "Relax pdb with allatom constraints" does not work with structures containing multiple chains

I am trying to use "Relax pdb with allatom constraints" to prepare starting files. This works fine as long as the input pdb contains only a single chain. If it contains two chains, relaxation fails (see attached log file). Although each of the component chains runs fine on its own, as soon as I try to process the complex, the process fails with a complaint about missing atoms:
"[ERROR] Exception caught by JobDistributor for job Graft_FV_0001_0001Atom CG 122 not found"

Post Situation: 

Rosetta 3.4 build error on Mac OS X Lion Intel Core i7

Dear All,

I got the source code of Rosetta 3.4. I am trying to compile it on Mac OS X 10.7.3 (Lion) Intel Core i7 with scons running the command "scons bin mode=release". At the end of the compilation I got this error (I include the last call to the compiler):

Post Situation: 

Is there any significant improvement of model generation in rosetta3.4 comparing to rosetta3.3?

I'm wondering whether there is improvement of model generation applications in rosetta3.4 (ex. make_fragment; abinitio, relax and etc.)? What are these improvements (Speed, Accuracy)?

Thank you very much!

Post Situation: 

Cluster gdtmm vs. rmsd

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?

Post Situation: 

Pages

Subscribe to RSS - Unsolved