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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">According to <a href="https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render">
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render</a> , 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.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Could you please suggest how to create this tunnel with variable width? Thank you.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Ondrej<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA
<o:p></o:p></p>
<p class="MsoNormal">HETATM 1 X TUN T 1 -45.770 -35.888 -4.154 0.00 2.01
<o:p></o:p></p>
<p class="MsoNormal">HETATM 2 X TUN T 1 -45.766 -35.893 -4.132 0.02 2.03
<o:p></o:p></p>
<p class="MsoNormal">HETATM 3 X TUN T 1 -45.762 -35.897 -4.111 0.04 2.11
<o:p></o:p></p>
<p class="MsoNormal">HETATM 4 X TUN T 1 -45.759 -35.901 -4.091 0.07 2.16
<o:p></o:p></p>
<p class="MsoNormal">HETATM 5 X TUN T 1 -45.756 -35.903 -4.073 0.08 2.14
<o:p></o:p></p>
<p class="MsoNormal">HETATM 6 X TUN T 1 -45.755 -35.903 -4.057 0.10 2.17
<o:p></o:p></p>
<p class="MsoNormal">HETATM 7 X TUN T 1 -45.756 -35.901 -4.045 0.11 2.10
<o:p></o:p></p>
<p class="MsoNormal">HETATM 8 X TUN T 1 -45.758 -35.896 -4.037 0.12 2.01
<o:p></o:p></p>
<p class="MsoNormal">HETATM 9 X TUN T 1 -45.763 -35.888 -4.032 0.13 2.01
<o:p></o:p></p>
<p class="MsoNormal">HETATM 10 X TUN T 1 -45.770 -35.876 -4.033 0.15 2.00
<o:p></o:p></p>
<p class="MsoNormal">HETATM 11 X TUN T 1 -45.779 -35.861 -4.037 0.16 1.99
<o:p></o:p></p>
<p class="MsoNormal">HETATM 12 X TUN T 1 -45.787 -35.843 -4.039 0.18 1.97
<o:p></o:p></p>
<p class="MsoNormal">HETATM 13 X TUN T 1 -45.794 -35.822 -4.034 0.21 1.95
<o:p></o:p></p>
<p class="MsoNormal">HETATM 14 X TUN T 1 -45.796 -35.800 -4.017 0.23 1.93
<o:p></o:p></p>
<p class="MsoNormal">HETATM 15 X TUN T 1 -45.792 -35.777 -3.984 0.27 1.92
<o:p></o:p></p>
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