The problem hasn't been solved
hello everybody!
I was wondering whether there is a way to get the gdt_ts using pyrosetta, unfortunately i cudnt find anything so far
tnx in advance
Hi RosettaCommons support group,
I have generated silent.out files using Rosetta 3.5 version to build homology models. I tried to extract the pdbs using the following script:
~/rosetta-3.5/rosetta_source/bin/extract_pdbs.macosgccrelease -database ~/rosetta-3.5/rosetta_database/ -in:file:silent silent.out -in:file:silent_struct_type binary -out:file:residue_type_set fa_standard, but could not and the error is as follows:
core.init: Mini-Rosetta version Split from developer trunk at 53488 from http://www.rosettacommons.org
Hello sir, I am installing rosetta w52 release, when i install Toolbox, it is automatically downloading the NMRPipe, Blast and Genome Database from nih site, and this process taking day by day, so please tell me is this compulsory for this or not??
In Supplementary Materials for
Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry
Herzog et al, Science 337, 1348 (2012)
the authors refer to the "ROSETTA nonlocal protocol" with a set of commandline flags:
------------------------------------------------------------------------------
Box S5: Command-line flags for ROSETTA’s nonlocal application. User specific command-line flags are given in curly brackets.
-database {rosetta_DB_dir}
-in:file:fasta {protein.fasta}
-in:file:psipred_ss2 {protein.ss2}
Sorry, but I don't see an explanation for this anywhere
Hi everyone,
I am a beginner in Rosetta and I am wondering if Rosetta could do ab initio folding of a metalloprotein with multiple metal ions.
I read the article by Wang et al.,(Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science) and was able to set constraints for one metal binding site in residue_pair_jump_cst file and run AbinitioRelax without any issues. However I have no idea how to set things up when two or more metal ions are involved. Do I also have to define every jump between those metal ions?
Hello,
My peptide sequence has a noncanonical aminoacid PCA combined with other canonical aminoacids.
I was wondering that anyway I can handle it properly in Rosetta.
Thanks
Hi,
Is multigraft available in Rosetta 3.5? It seems on this page https://www.rosettacommons.org/software, it's available in 3.5. But there's no documentation for it in the manual for 3.5. Thanks!
Hello,
I applied the FlexPepDock refinement protocol and the FlexPepDock ab-initio protocol to simulate the same peptide-protein complexe(1K5N) and generated a mass of models(refinement n=1000; ab-initio n=50000). The score function of two protocols is score12. The models was ranked based on the reweighted-score.
However, the score of the top models of refinement is better than ab-initio.Sub-angstrom models were sampled in the cases of refinement. Even though ab-initio protocol generated near-native models,their energy score is high.
I am building rosettaligand for boinc. Compiling linux versions are straightfoward and easy. But when on windows, life is like in the hell. I hacked a few things to get static rosettaligand version built under cygwin on windows7 32bit, and it run smoothly under cygwin emulator. However, when I tried to run rosettaligand from windows commandline prompt, it said "ERROR: Unique best command line context option match not found for -path. Possible matches include: in:path out:path". I changed the line terminator and remove all path seperator in flags file, but the error persisted.