[Chimera-users] Drawing shapes given coordinates

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 4 14:20:45 PST 2016

Hi Rebecca,
There are two approaches for adding cylinders independent of atoms… but I don’t know if either will be satisfactory:

(1) “shape cylinder” is command-line and doesn’t require using atoms as endpoints, but it doesn’t allow specifying endpoint coordinates directly.  A cylinder is specified by only its center, height, radius, and a rotation angle.  I don’t think it is easy to figure out what angle gives the desired endpoint coordinates.  (We’ve discussed the need to improve this, but it may be deferred to our next-generation software in development.)

(2) BILD-format input allows specifying endpoint coordinates of a cylinder, but it is not a command.  You generate a BILD text file describing the objects and read it in to Chimera.  BILD format is very simple, however:

The objects created with “shape” are surface models, so you can change their colors afterward.  The BILD objects are not surface models and cannot be recolored and do not work well with transparency. 

There are two approaches that depend on atoms:

(1) pseudobonds can be created with the “distance” command (or atom pairs can be read in from a file with Pseudobond Reader), but pseudobonds require atoms as endpoints.

(2) the “define” command (or Axes/Planes/Centroids) tool will show cylindrical axes that are best fits to specified sets of atoms.  However, there is currently little control over length… it is automatically determined from the atomic coordinates.

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 Jan 4, 2016, at 12:09 PM, Rebecca Swett <Rebecca_Swett at vrtx.com> wrote:
> Hi all, 
> I'm trying to add some 3d shapes to a visualization. I was wondering if it would be possible to draw either a cylinder or tube given starting and ending coordinates rather than atom names/numbers or centroid? For example, if I had this coordinate pair:
> 6.17 1.10 -15.33     20.82 -0.70 -8.39
> What would be the best way to go about drawing a line of some sort between those two points? I have dozens of pairs of coordinates so something command line would be ideal. 
> Cheers,
> Rebecca

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