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

Tue Nov 22 14:11:05 PST 2016

Hi Elaine,
Thank you for the clarification. It works now.
Actually, I set Value equal to Atom radius (e.g. 2.01 and 2.01). It gives me a chain of balls with variable diameter which perfectly fills the tunnel. Then I calculate the surface of the chain, set its transparency and hide the rest.
Best,
Ondrej

From: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Sent: Tuesday, November 22, 2016 8:51 PM
To: Kuda Ondřej <Ondrej.Kuda at fgu.cas.cz>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Render by Attribute - Radii and individual radius for each HETATM

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 at 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#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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Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Physiology CAS. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract; nor does it create any pre-contractual liability on the part of Institute of Physiology CAS.