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matdes_design: ERROR]EXCN_utility_exit has been thrown from: src/core/io/silent/SilentFileData.cc line: 302

Submitted by siciliu on Fri, 2014-03-21 17:51

Hi all,

I'm trying to do a test run of matdes_design with the following flags:
-database /local/databases/minirosetta/ -s 3N79_edit.pdb -symmetry_definition O3.sym -ex1 -ex2 -holes::dalphaball ../../../DAlphaBall_new/src/DAlphaBall.icc -matdes::pdbID 3n79 -matdes::prefix O3_ -matdes::num_subs_building_block 3 -matdes::num_subs_total 24 -matdes::radial_disp -20 -matdes::angle 6 -ignore_unrecognized_res True -matdes::design::grid_size_angle 2 -matdes::design::grid_size_radius 2 -matdes::design::grid_nsamp_angle 5 -matdes::design::grid_nsamp_radius 11

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Noncanonical amino acids

Submitted by wsgosal on Tue, 2014-03-18 05:29

Hi all,

I am trying to implement the method outlined in "Incorporation of Noncanonical Amino Acids into Rosetta and use in Computational Protein- Peptide Interface Design" doi:10.1371/journal.pone.0032637.

I just wondered if I should start right from the beginning, or whether there is somewhere I can download the parameter files, rotamer libraries and unfolded state reference energies for NCAAs so that I can move directly to doing the design protocol.

Any advice would be most appreciated.

wsgosal

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Reproducing Rosetta++ scoring function with Rosetta 3?

Submitted by JuliusSu on Mon, 2014-03-17 21:15

Dear Rosetta developers, I am wondering whether it is possible to cross-check results between Rosetta++ and Rosetta 3 by using the same scoring function for each.

As an example, I tried evaluating the score of the attached PDB file using the two programs and obtained -79.88 from Rosetta++ and 323.668 from Rosetta 3. I also tried breaking down the energies into components to resolve the difference, without much success.

I've attached a more detailed output below.

The reason I am trying to do this is our lab would like to make use of the protocol outlined in

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running Rosetta locally using commands generated by the Robetta web server

Submitted by cneale on Sat, 2014-03-15 11:48

Dear Rosetta users:

I ran a full structure prediction on the Robetta web server and obtained useful results. Now I would like to run Rosetta locally (because I want to control the fragment libraries).

I installed Rosetta3.5 and did a test run, but the locally-generated structures are quite different than those that I obtained from the Robetta web server (the Robetta results are much better). I presume that this is because I have not configured the local Rosetta run very well.

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Options for Enzdes RosettaScripts

Submitted by joeg on Wed, 2014-03-12 09:28

Hello,

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Trouble linking with Xcode/clang 5.1

Submitted by stranges on Tue, 2014-03-11 09:34

Hi all,
Just a heads up. There's a problem linking with the new OSX Command Line Tools and clang version 5.1.
This is with the most recent weekly release 2014 week 04
Any suggestions would be appreciated

Clang version:
clang --version
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

Error message

Undefined symbols for architecture x86_64:
"core::io::silent::ProteinSilentStruct_Template::fill_struct(core::pose::Pose const&, std::string)", referenced from:

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Rosetta 3 - Build/Install

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Does RNA parses checkpoint matrix as well as protein

Submitted by qlj on Wed, 2014-03-05 06:03

Hi,

I am recently studying Rosetta for rna prediction.

When Rosetta make fragments for proteins, there are a step to prase a PSI-BLAST binary checkpoint file. The output likes as follows:
G 0.0783 0.0108 0.0337 0.0256 0.0162 0.5101 0.0135 0.0189 0.0337 0.0283 0.0094 0.0391 0.0189 0.0189 0.0229 0.0513 0.0297 0.0243 0.0054 0.0108
S 0.1099 0.0175 0.0489 0.0524 0.0209 0.0663 0.0192 0.0297 0.0541 0.0419 0.0157 0.0541 0.0297 0.0332 0.0401 0.2199 0.0820 0.0419 0.0052 0.0175

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unwanted Glycines after PackRotamersMover

Submitted by oppopomoz on Tue, 2014-03-04 10:08

Hello everybody.

I am trying to design the sequence of small peptides (4-8 aa long) using PackRotamersMove but I tend to get way too many glycines (50% of residues become Glycines as avarage).
here my protocol:

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
scorefxn_12 = create_score_function_ws_patch('score12','score12')
task_design = TaskFactory.create_packer_task(pose)
parse_resfile(pose, task_design,"resfile")
pack_design = PackRotamersMover( scorefxn_12, task_design )
pack_design.apply(pose)
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

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PyRosetta - Scripts

InterfaceAnalyzer problem

Submitted by almeida on Mon, 2014-03-03 14:56

Hi all, I'm trying to run InterfaceAnalyzer in the "classical" and xml script modes. In the "classical" mode I ran: > InterfaceAnalyzer.linuxgccrelease @flags_IL2_Q74P_2 ... with this flags: -in:file:l ../IL2_IL2Ra_new_0001.pdb -in:file:fullatom -compute_packstat true -tracer_data_print true -out:file:score_only score.sc -use_resfile yes -resfile IL2_Q74P.resfile -fixedchains A B -pack_input false -pack_separated true -add_regular_scores_to_scorefile true -use_jobname true -database /home/almeida/Softwares/Rosetta/rosetta_3.4/rosetta_database

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