[Chimera-users] Drawing shapes given coordinates
Rebecca_Swett at vrtx.com
Tue Jan 5 05:37:16 PST 2016
Thank you! Theoretically if I was to create dummy atoms with coordinates
at the locations where I want the cylinders to end, I could connect them
with pseudobonds. I can easily shape my data that way, and if it doesn't
work the BILD files will probably be fine. Thanks for the help!
On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>There are two approaches for adding cylinders independent of atomsŠ but I
>don¹t know if either will be satisfactory:
>(1) ³shape cylinder² is command-line and doesn¹t require using atoms as
>endpoints, but it doesn¹t allow specifying endpoint coordinates directly.
> A cylinder is specified by only its center, height, radius, and a
>rotation angle. I don¹t think it is easy to figure out what angle gives
>the desired endpoint coordinates. (We¹ve discussed the need to improve
>this, but it may be deferred to our next-generation software in
>(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
>The objects created with ³shape² 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 ³distance² command (or atom pairs
>can be read in from a file with Pseudobond Reader), but pseudobonds
>require atoms as endpoints.
>(2) the ³define² 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 lengthŠ 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>
>> 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.
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