[Chimera-users] Drawing shapes given coordinates

[Rebecca Swett]

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!
Cheers,
Rebecca

On 1/4/16, 5:20 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

>Hi Rebecca,
>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
>development.)
><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi
>mera_docs_UsersGuide_midas_shape.html-23cylinder&d=CwIFaQ&c=TzEZu9LIcihmW3
>7vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd
>4eXf6HdP_BL9dt0gv_zz3oMdq8&s=9vZCIh2K2i-8UrGF7HkSZwZwT7CRFcS9RUZsHUsson4&e
>= >
>
>(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:
><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi
>mera_docs_UsersGuide_bild.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r=Z2BqCMu
>wlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_BL9dt0gv_
>zz3oMdq8&s=2A5wPT06BJ7QN1TDyA4kS36ILONzhA703a7xRpdnJKY&e= >
>
>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.
><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi
>mera_docs_UsersGuide_midas_distance.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w
>&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP
>_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= >
><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi
>mera_docs_ContributedSoftware_pbreader_pbreader.html&d=CwIFaQ&c=TzEZu9LIci
>hmW37vx9Ah6w&r=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH
>6akd4eXf6HdP_BL9dt0gv_zz3oMdq8&s=nRvWQ2FPg5n33Obqd9Bee1ovSNmgCCdbaT1EH6Uc1
>I8&e= >
>
>(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.
><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chi
>mera_docs_UsersGuide_midas_define.html&d=CwIFaQ&c=TzEZu9LIcihmW37vx9Ah6w&r
>=Z2BqCMuwlxQxgSzUiCDaK4rAd15j9FSes0phjplcAGU&m=ALnOY5nR3xnyH6akd4eXf6HdP_B
>L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= >
>
>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 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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