User Tab

In this tab you can choose user-generated or modified Rosetta and Shell script templates.

_images/user_tab.png

Rosetta

In this box user-defined Rosetta XML script template can be choosen.

  • Select: An external Rosetta XML script template can be located on the filesystem.

  • Replace default Rosetta script template: Enabling this check box forces StarMap to use the choosen template instead of the default one when generating the execution scripts.

Shell

In this box user-defined Rosetta shell script template can be choosen.

  • Select: An external shell script template can be located on the filesystem. Template filenames must contain the keyword local or cluster. Once choosen this template will be added to the pull down menue in the corresponding Save tab based on the keyword. This shell script generation is independent of the choosen Rosetta XML script.

As an alternative predefined templates can be put in a special folder as described in the Templates section.

StarMap Replacement Values

StarMap uses the following replacment values. This keywords can be used also in user-defined script templates. For easier visuability the patterns start and end with @@ in both Rosetta and shell scripts.

The following patterns are valid and case sensitive:

  • @@CONSTRAINT_SET_FILE@@: The path and filename of the selected constraint set.

  • @@DENSITY_FILE@@: The density map file.

  • @@HIRES@@: The density map resolution.

  • @@USE_SYMMETRY@@: Run symmetry options.

  • @@INPUT_PDB_FILE@@: The filename of the saved selection from ChimeraX.

  • @@NSTRUCT@@: The number of output models.

  • @@ROSETTA_SCRIPT_EXE@@: The filename of the used Rosetta script executable (e.g. rosetta_scripts.default.linuxgccrelease).

  • @@ROSETTA_SCRIPT_FILE@@: The filename of the used Rosetta XML script.

  • @@STRATEGY@@: The rebuilding strategy, either auto or user.

  • @@SYMMETRY_FILE@@: If you run the symmetry check, the output filename will replace this pattern.

  • @@VALIDATION_HALF2_FILE@@: The second half-map for the model evaluation.

In the XML file use e.g.:

<LoadDensityMap name=loaddens mapfile="@@DENSITY_FILE@@"/>

Or in the runtime shell script this parameter can be set with the command line option:

-edensity:mapfile @@DENSITY_FILE@@

User-defined Replacement Values

StarMap provides 8 user-defined replacement tokens with the naming @@USER1@@ up to @@USER8@@. This tokens can be used in Rosetta XML and shell script templates. During the execution script generation this tokens will be replaced by the changed user interface values.

To customize the StarMap GUI the label tokens can be overridden by environment variables with the corresponging number e.g.:

export STARMAP_USER8="dens_weights"

The environment values STARMAP_USER1 and STARMAP_USER2 can be overriden as above, but if the values are not set or empty they will be preset by extra_res_cen and extra_res_fa to make the ligand support with the corresponding template easier for users.

If set the GUI would change like in the following image:

_images/user_tab_var.png

Ligands

If you want to use more ligands during the refinement do:

For extra_res_cen and extra_res_fa, simply add multiple entries:

-extra_res_fa LG1.params LG2.params

For -extra_improper_file, cat all the files together:

cat LG1.tors LG2.tors > all.tors

and use that file as input.

Newer versions of Rosetta (3.10+) no longer need the -extra_improper directive (specifying it will not hurt however).

If you use the Rosetta script molfile_to_params.py to generate the params files, it’s located in:

${ROSETTA3}/source/scripts/python/public/molfile_to_params.py