[Chimera-users] Drawing shapes given coordinates

Oliver Clarke olibclarke at gmail.com
Thu Jan 7 08:49:13 PST 2016

Dear Rebecca, I have used Elaine's suggestion before, and it works
well, as in  the following alias:

alias ^pbond dist sel; setattr p label "" sel; setattr p drawMode 1
sel; setattr p radius 0.03 sel

which places a thin black cylinder between two selected atoms.

To make invisible dummy atoms at arbitrary coordinates, I would use
the "mc" accelerator ("ac mc" on the command line), which places and
selects a dummy atom at the center of rotation.

So something like: cofr x1,y1,z1; ac mc; namesel atom1; cofr x2,y2,z2;
ac mc; namesel atom2; sel atom1|atom2; pbond; vdwdefine 0.01 sel;
transparency 100,a sel

should work.



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
<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>> 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
*>*= >
*>>*(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:
*>*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.
*>*_BL9dt0gv_zz3oMdq8&s=tUGhl0z5yTsTqr2tyEgexdraCTB8o2JtwjuJZTgMwvo&e= >
*>*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.
*>*L9dt0gv_zz3oMdq8&s=t9I-WC_-VvEvmTfphtU3ey2GT0sMRiFtO62hFkRj7Rk&e= >
*>>*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 <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>>
*>>>>* 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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