Hi,
This is a fairly basic question about syntax. How does one: as surface the
protein and pseudoatoms in the short script below? Moreover, and work with
the Lysine amines rather than the alpha carbons?
# for_gnp.py
# fetch a protein and create whole phage
cmd.fetch("1ifp", type="pdb1", multiplex=1, async=0)
# make a blank list
l=[]
# iterate over all lysine's alpha carbons
cmd.iterate_state(1, "n. CA and resn lys", "l.append((x,y,z))")
# set a counter to 0 for controlling unique names
p=0
# iterate over all coordinates and create a
# pseudoatom at each lysine's alpha carbon
for ca in l:
p+=1
cmd.pseudoatom("pseudo%s" % (p), pos=ca, vdw=5.0)
# measure the pairwise distances across all pseudoatoms just created
cmd.distance("/pseudo*", "/pseudo*")
Many thanks,
James
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