Compiling RosettaHoles on mac:
CPU=macgcc NAMEFUL1=$(DIR)/$(NAME1).$(CPU) FC = /usr/local/bin/gfortran-4.9 FFLAGS = -c -O3 -x f77-cpp-input -fsecond-underscore CC = /usr/local/bin/gcc-4.9 LD = /usr/local/bin/gcc-4.9 CFLAGS = -c -O3 LDFLAGS = -O3 LIBRARIES= -lgmp -lm -lgfortran INCS= -I/usr/local/include LIBS= -L/usr/local/lib
Command Line
Visualization in PyMOL
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='+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='+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)
Representative Image
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