[Chimera-users] Creating a dummy atom on a defined position

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 11 13:36:29 PDT 2016

Hi Subha,
What’s easiest depends on whatyou want to do.  If it is just for display purposes, the easiest is to just use “shape sphere,” but that will not allow you to do stufff like measure distances.  The “shape” command creates a surface model, not an atom.  Example command:

shape sphere center 1.5,2.2,0.0

… where the 3 comma-sep numbers are the coordinates.  You can also specify which coordinate system they should be interpreted in, if you have other models open that have been moved separately from one another.  See the “shape” manpage:

If you actually wanted to measure distances from that point, however, you would need to add a marker or atom at the coordinates.  Unfortunately there is no command equivalent to adding an atom with specific coordinates like you can do in the Build Structure GUI.  I did come up with a rather horrible kludge to add a marker at specific coordinates.  A marker allows measuring distances but it is not exactly the same as an atom (it's not good for structure-building).  The horrible kludge is to make a fake volume model using a specific origin, put values into that volume model, and then measure its center (which allows putting a marker at that position).  What’s even worse is that you have to offset the origin of the fake map from the coordinates that you want the marker, because the origin is not the same as the center.  For example, here’s a command file to put a marker at 1.5,2.2,0.0:

# subtract 1.00,1.01,1.00 from desired coordinates to give needed origin
vop new junk origin 0.5,1.19,-1.00 size 3 model #10
mask ones #10 model #11
measure center #11 mark true model #12
close #10,11
getcrd #12

(the last command just reports the coordinates, as a check… I expected the need to subtract 1,1,1 but why the middle value needs to have 1.01 subtracted is a mystery to me… determined empirically)


I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Oct 11, 2016, at 12:03 PM, Subha Kalyaanamoorthy <kalyaana at ualberta.ca> wrote:
> Hi There,
> Wondering if there is a way to create a dummy atom on a specified position(xyz coords) using a chimera command line?
> Thanks,
> Subha

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