<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">You can also use the "slab" option with command "shape rectangle" to get a 3D box, for example,<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>shape rectangle width 40 height 50 slab 30<br class=""><div><br class=""></div><div>But it does not give sharp edges between the xy box sides (see image).</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><img apple-inline="yes" id="0C234AFC-C1C1-4B97-88AE-07A10C3195FD" width="457" height="391" src="cid:042269A9-21B3-421C-B8F4-D92F847F1A78" class=""><br class=""><blockquote type="cite" class=""><div class="">On Feb 23, 2022, at 12:25 PM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Gustavo,<br class="">There are a few different possibilities:<br class=""><br class="">(1) create a BILD format file describing geometric objects. It is a simple plain-text format described here, typically just created in the text editor of your choice, and you would name the file something.bild and open it in ChimeraX to display the objects.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html</a>><br class=""><br class="">(2) create markers and links, which are essentially fake atoms and bonds. They can be created within ChimeraX using the "Marker Placement" tool or "marker" command, or you can use your own external process to create a marker file and then open it in ChimeraX.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/markers.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/markers.html</a>><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html</a>><br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html</a>><br class=""><br class="">(3) create shapes which are surface models, using the "shape" command:<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html</a>><br class=""><br class="">Shape does not have cube option, although you could create a box from repeated use of the "triangle" or "rectangle" option. Still it may make more sense to use one of the other methods to draw a box. If you are using "shape" it may be easier to use triangles to make the box than rectangles, because the triangle option allows specifying the vertex coordinates whereas the rectangle location has to be specified by its center.<br class=""><br class="">(4) create a cube as a surface with only 8 vertices, using Python somehow (sorry somebody else would have to advise on how to do this)<br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D. <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><br class=""><br class=""><blockquote type="cite" class="">On Feb 23, 2022, at 11:31 AM, de Miranda Seabra, Gustavo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi,<br class=""><br class="">I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc. <br class=""><br class="">How to do this in ChimeraX?<br class=""><br class="">Thanks a lot!<br class="">--<br class="">Gustavo Seabra<br class="">Research Associate Professor<br class="">Center for Natural Products, Drug Discovery, and Development (CNPD3)<br class="">Department of Medicinal Chemistry<br class="">College of Pharmacy<br class="">University of Florida, Gainesville, FL, USA<br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>