Dear all,
I am building a model using a low-resolution (>15A) cryoEM map. How can I compute the CC (or similar) with Rosetta?
Thanks
Hello,
I am trying to calculate the per residue SAP scores of a protein structure using Rosetta scripts. The .xml script I am using is shown below.
<ROSETTASCRIPTS>
<SCOREFXNS>
</SCOREFXNS>
<RESIDUE_SELECTORS>
</RESIDUE_SELECTORS>
<FILTERS>
</FILTERS>
<SIMPLE_METRICS>
<PerResidueSapScoreMetric name="sapscore"/>
</SIMPLE_METRICS>
Hello everyone, while running a scoring file, I entered the following command line:
Hi, everyone!
I am performing protein-protein docking with AtomPairConstaint (the experiment shows the distance between two ligands) and I have some questions:
a. Whether the ref2015 or ref2015_cst function considers the ligand (with params file)?
b. If I use ref2015_cst in the docking_protocol, does the score function consider the constraint weight in both low- and high-resolution stages?
I am running the Rosetta version - rosetta.source.release-334.tar.bz2 for designing two proteins but no values are generated for the total score. All the important files regarding this are attached. Please look at it and help me with this.
Hi,
using a flag containing options "-dunbrack_prob_buried_semi 0.8" and "-dunbrack_prob_nonburied_semi 0.8", errors appear like:
...................................
File: /home/shanghai/RationalDesign/Rosetta3.9/rosetta_src_2018.09.60072_bundle/main/source/src/utility/options/OptionCollection.cc:1314
Option matching -dunbrack_prob_buried_semi not found in command line top-level context
...................................
the flags and log file were attached.
Please help, thanks
Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
So far I thought the soft score function is supposed to feature lower repulsive terms.
ref2015_soft.wts:
Greetings,
I ran a design protocol and I find my results score has high fa_sol scores like 250 around. What should I do to lower down the fa_sol scores?
I used ResidueSelector to separate my alpha-helixs into three parts: buried, semi-buried and solvent exposure. And use resfiles to assign the amino acids, buried------hydrophobic, semi-buried------less hydrophobic, solvent exposure-------hydrophilic.
And I am wondering if the fa_sol score of a model is too high, will it be insoluble in water after experimental expression?
