Hi Ondrej, Firstly, you should be using “bfactor” not “occupancy” since your radius values are in the bfactor column. Secondly, these points are all extremely close together, so if you really use the radius values shown in your file, all you will see is one sphere because all the centers are inside of it…. i.e. to be able to see a tunnel shape you would need to use much smaller radii. I mapped your value 1.92 to actual radius 0.0384 and your value 2.17 to actual radius 0.0434 (20% as large) and then I could see the tunnel shape. The Render by Attribute dialog is kind of annoying in that it won’t let you easily enter atom-radius values smaller than 0.1. You have to first enter something like .384 and then insert the zero before the 3. I also used the Color part of the dialog to color from yellow (smallest) to red (largest) and attached an image of the results below. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 22, 2016, at 4:39 AM, Kuda Ondřej <Ondrej.Kuda@fgu.cas.cz> wrote:
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... , 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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