[Chimera-users] Drawing shapes given coordinates

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 5 10:45:23 PST 2016

You’re welcome!

If going the pseudobond route, just make sure you can get the kind of display you want.   If you just want solid cylinders, that can be achived with the stick drawmode, and you can also set color and radius as desired.  If you make a file for Pseudobond Reader you can also specify the colors and (optional) text labels in the file.   Otherwise you can control  pseudobond attributes collectively or individually with “setattr p” and “setattr g” commands.

For example, you could hide all distance labels with command: setattr p label ''

(that’s two single quote marks in a row) and the same command except plus “sel” at the end will do it for only the pseudobonds with both end atoms selected.  You could also give the atom names.

> On Jan 5, 2016, at 5:37 AM, Rebecca Swett <Rebecca_Swett at vrtx.com> wrote:
> 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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