Analysis Tab

On this tab previous generated or external data can be analyzed.

_images/analysis_tab.png

Rosetta Results

After a successful run of Rosetta the result PDBs can be sorted based on the FSC value by pressing the Execute button. This means the PDBs with the best value get re-ordered to the name starmap_result_0001.pdb, the second best to …0002.pdb etc.

Analysis

Here you can select the external input data for analysis.

Density

The input density map for the FSC calculation. This value will be preset with the same one as in the Rosetta tab. You can choose a different one by pressing the Select button.

If a half2 map was choosen in the Advanced tab, you should use here also the half2 map here (if not already preset).

Rosetta Result PDB

Select the input PDB file for the analysis.

Resolution

The Map resolution value is preset from the Rosetta tab and can be set if external input data are used.

Graphs

  • Execute: Choose on which values the FSC will be calculated. The calculation can be 5 seconds up to 5+ minutes depending on your input data and chosen option. ChimeraX is blocked during the execution. When the calculation is finished the Preview button changes its color.

    After the execution StarMap prepares multiple .cxc scripts for coloring of the Z-score values in the working folder for highlightning ribbons in ChimeraX. To use it open the input .pdb file first and then open the corresponding .cxc file.

    The generated .vsz files can be loaded in the Veusz program to generate professional graphs. The .vsz files need also the assoziated .csv files in this directory.

  • Preview: Based on the selected option the corresponding graph will be shown in a pop-up window. If the results contain multiple chains, a image for each chain will be generated.

Cleanup

  • Cleanup: Deletes the .err and .out files and intermediate script files.

Notes on Z-score

If you run the LCC per residue the LCC zscore per residue calculation is also done.

The Z-score in StarMap comes from the sum of four values that are calculated separately and weighted differently:

Z_density Z_neighborhood_density Z_rama Z_bondstrain

The combined score uses weights of 0.45, 0.05, 0.15, and 0.35 on these terms respectively.

So Z-score = Z_density*0.45 + Z_neighborhood_density*0.05 + Z_rama*0.15 + Z_bondstrain*0.35