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Which score4?

Submitted by oppopomoz on Tue, 2013-03-12 06:21

Hello everybody.

I read that the final step in the low-resolution part of a rosetta classic ab-initio protein fold prediction protol should be rescoring the obteined structures with the score4 in order to discriminate the native-like structures.

Looking for this score4 I could find the following score4-like scores (both in the pyrosetta package and rosetta3.4 package): "score4L", score4_smooth", score4_smooth_cart".
In all papers I've read I could not find any references to any of them but only to "score4". Does anybody know which this "score4" is?

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PyRosetta - General

CS-HM-Rosetta

Submitted by pwurm on Thu, 2013-03-07 12:56

Hello,

i would like to use the CS-HM-Rosetta for homology modelling with chemical shift data. It is stated in the supporting information (http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1202485109/-/DCSupplem...) that cm_scripts/rosetta_cm.conf needs to be edited before the execution of "cm_scripts/bin/predict_distances.pl sequence.fasta sequence.aln –aln_format grishin –outfile sequence.dist_csts" in order to generate the homology constraints.

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Rosetta 3 - Applications

Score2 and Score5...aren't hey meant to be different?

Submitted by oppopomoz on Wed, 2013-02-20 03:31

Hello everybody

doing
score_fxn5=create_score_function( 'score5' )
score_fxn2=create_score_function( 'score2' )

and printing them I obtain the same output, I thought they were meant to be different.

print score_fxn?
ScoreFunction::show():
weights: (vdw 1) (cenpack 0.5) (pair 1) (env 1) (cbeta 0.25) (hs_pair 1) (ss_pair 1) (sheet 1)
energy_method_options: EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT
EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12
EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid

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PyRosetta - General

Results of enzyme_design not consistent with Resfile

Submitted by yogeshkd on Thu, 2013-02-14 15:56
Hi all, I am running the enzyme_design application with one input Resfile and no cstfile. I know for the fact that the Resfie is being read based on the output, part of which is shown here: **** protocols.enzdes.EnzdesTaskOperations: Reading resfile input from: mutations.resfile protocols.enzdes.EnzdesTaskOperations: Design Interface: detected 0 design-shell residues and 68 repack-shell residues, shell sizes cut1-4 used were 0 0 10 12 **** The relevant part of options file (the indentation is correct in the original file): **** -resfile mutations.resfile -enzdes
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Rosetta 3 - Applications

fixing disulfides in homolgy modeling

Submitted by pdbb on Wed, 2013-02-13 11:43

Hi,

I am running Rosetta for predicting a structure of a protein (target) using a homologous protein (template). The template does not cover the whole target structure. The parts that are not covered contain cysteins. Is it possible to fix those residues in a disulfide bridge? When I use -in:fix_disulf option, I get an error message:

"core.conformation.Conformation: [ERROR] Residue 322 is out of range."

I think Rosetta is fixing residues in the template, but not in the target protein. Is it possible to fix disulfides in the target protein?

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