[Chimera-users] Render by Attribute - Radii and individual radius for each HETATM

[Kuda Ondřej]

Hello,
I have a path (chain of heteroatoms with defined radii, see below) forming a pore in a protein. I would like to create an envelope (surface view) to illustrate the 3D path within the protein. My problem is that Chimera uses default vdw value and not the values I defined. Therefore, the "pore" has a constant diameter.

According to https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render , I tried "Render by Attribute  - Occupancy - Radii". I assumed that the VDW values are rendered for each HETATM according to the input, but it seems that the VDW values are sorted (smallest > largest) and then applied on the chain starting from #1. Therefore, it creates kind of a funnel structure.

Could you please suggest how to create this tunnel with variable width? Thank you.

Best,
Ondrej

REMARK ATOM  NAM RES   TUNID     X       Y       Z    Distnm RadiusA
HETATM    1  X   TUN T   1     -45.770 -35.888  -4.154  0.00  2.01
HETATM    2  X   TUN T   1     -45.766 -35.893  -4.132  0.02  2.03
HETATM    3  X   TUN T   1     -45.762 -35.897  -4.111  0.04  2.11
HETATM    4  X   TUN T   1     -45.759 -35.901  -4.091  0.07  2.16
HETATM    5  X   TUN T   1     -45.756 -35.903  -4.073  0.08  2.14
HETATM    6  X   TUN T   1     -45.755 -35.903  -4.057  0.10  2.17
HETATM    7  X   TUN T   1     -45.756 -35.901  -4.045  0.11  2.10
HETATM    8  X   TUN T   1     -45.758 -35.896  -4.037  0.12  2.01
HETATM    9  X   TUN T   1     -45.763 -35.888  -4.032  0.13  2.01
HETATM   10  X   TUN T   1     -45.770 -35.876  -4.033  0.15  2.00
HETATM   11  X   TUN T   1     -45.779 -35.861  -4.037  0.16  1.99
HETATM   12  X   TUN T   1     -45.787 -35.843  -4.039  0.18  1.97
HETATM   13  X   TUN T   1     -45.794 -35.822  -4.034  0.21  1.95
HETATM   14  X   TUN T   1     -45.796 -35.800  -4.017  0.23  1.93
HETATM   15  X   TUN T   1     -45.792 -35.777  -3.984  0.27  1.92

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