[PyMOL] [pymol] Wrong Visualization of set Spheres

[Julian K. <s2j...@un...>]

Dear Pymol-Team,

very new in this forum i come along with a specific problem.
I wrote a little pymol-script:


load /work/jkrumm/edgelook/0.00M/cter/40-helix-edge/helix-40.pqr

hide lines
show cartoon

radius = 2.7
vdw_a = 2.7

for i in range(401,413,1):\
 print(i)\
 vdw_a = vdw_a + 2.7\
 print(vdw_a)\
 cmd.create("helix%d" % i, "/helix-40///PRT`%d/PRT" % i)\
 cmd.alter("helix%d" % i, expression="vdw=%d" % vdw_a)
rebuild

disable all


for i in range(401,413,1):\
 cmd.set(name="sphere_transparency", value=0.0, selection="helix%d" % i)\
 cmd.show(representation="sphere", selection="helix%d" % i)\
 cmd.enable(name="helix%d" % i)

enable helix-40

set_view (\
     0.246392056,   -0.601405144,    0.760001123,\
    -0.951444209,   -0.299392790,    0.071540825,\
     0.184513614,   -0.740724683,   -0.645971537,\
     0.000000000,    0.000000000, -270.700958252,\
     0.528925896,    8.660091400,   -2.648437977,\
   100.995597839,  440.406250000,  -20.000000000 )

bg_color white
set reflect, 0
png ./test.png, width=2400, height=1200, dpi=300, ray=0


It is reading the PRT-entrys out of the input file to new objects and then
adjusts the proper radius.
The radius of the protein spheres is incremented by 2.7 Å. Moreover the
sphere center is shifted away from the C-terminus towards the N-terminus
by a distance equal to its radius (not done by pymol).
This should lead to the situation, that the surfaces of all
protein-spheres cut succinctly in one point at the C-Terminus, which they
do not.
It comes to slightly deviations when the spheres are getting visualized.

I already checked the sphere-centers. They are placed right. Also the
radii are set right. After i showed this to my advisor he is the same
opinion that the problem has to be pymol-based. I can't explain and i hope
You are able to help me with this problem.

Attached to this mail You will find the pymol-session and the input PQR.

Sincerely,
JuK


P.S. If i broke any rule of support-requesting or if any information is
missing please let me know.