The RosettaHoles API runs the RosettaHoles application (described here: https://pubmed.ncbi.nlm.nih.gov/19177366/ See RosettaHoles for details) on an input PDB file. RosettaHoles is an application which identifies voids in protein structures. It is useful for evaluating the quality of protein designs, among other things. It is recommended that the Clean PDB API be used to pre-process any PDB file which was

Quickstart

cyrus engine submit rosetta-holes input.pdb

Inputs

• --pdb-file

  • Input PDB file - cleaned and/or relaxed (especially for any PDB not originally generated by Rosetta

...

Running RosettaHoles

RosettaHoles can be run with the following command:

cyrus submit rosetta-holes input.pdb

The job takes a few minutes to run and produces two outputs:

• a

  • )

  • Prepare a clean PDB using the Clean PDB API

Outputs

• *_cavs.pdb

  • PDB file with voids indicated as virtual

  Atomsthe rosetta logs, which contain

  • AToms

  • The file will be prefixed by the file name of the original input pdb.

• logs.txt

  • Rosetta logs containing a variety of scoring information

Notes

Interpreting Output

The holes in the output PDB are indicated using virtual HETATM records at the end of the PDB file, all of which have the atom name V, the resid CAV and chain Z. The radius of each void in Å is stored in the b-factor column of the PDB file.

The script below can be loaded into pymol to add some useful commands for interacting with the virtualAtoms. In particular the showPacking command will set the radii of all protein atoms to the vdw radius used by Rosetta, and will set the radii of the CAV virtual atoms to the values set in the b-factors.

from pymol import cmd

def useRosettaRadii():
    cmd.alter("element C", "vdw=2.00")
    cmd.alter("element N", "vdw=1.75")
    cmd.alter("element O", "vdw=1.55")
    cmd.alter("element H", "vdw=1.00")
    cmd.alter("element P", "vdw=2.15")
    cmd.alter("element S", "vdw=1.90")
    cmd.alter("element RE", "vdw=1.40")
    cmd.alter("element CU", "vdw=1.40")
    cmd.set("sphere_scale", 1.0)

def expandRadii(delta=1.0, sel='all'):
    for a in cmd.get_model(sel).atom:
        r = float(a.vdw) + float(delta)
        cmd.alter("index "+a.index,'vdw='+str(r))
        cmd.rebuild(sel,"spheres")

def contractRadii(delta=1.0, sel='all'):
    for a in cmd.get_model(sel).atom:
        r = float(a.vdw) - float(delta)
        cmd.alter("index "+a.index,'vdw='+str(r))
        cmd.rebuild(sel,"spheres")

def useTempRadii(sel="all"):
    for ii in range(30):
        radius = "%0.1f"%(float(ii+1)/10)
        cmd.alter(sel+" and b="+radius,"vdw="+radius)
        cmd.rebuild()

def showpacking(sel="all"):
    useRosettaRadii()
    useTempRadii(sel+" and resn CAV")
    cmd.hide('everything', sel+" and resn CAV" )
    cmd.show('spheres', sel+" and resn CAV" )

cmd.extend('useRosettaRadii', useRosettaRadii)
cmd.extend('expandRadii',expandRadii)
cmd.extend('contractRadii',contractRadii)
cmd.extend("useTempRadii",useTempRadii)
cmd.extend("showpacking",showpacking)

References

RosettaHoles Application