[Chimera-users] Slicing/Subdividing Models in Chimera

Tom Goddard goddard at sonic.net
Mon Feb 4 14:13:48 PST 2019

Hi Jon,

  The command to show a subregion of a volume looks like

	volume #1 region 0,0,0,85,100,50

where the 6 numbers are the two corners in grid index units.  You would need to look at the size of your grid (shown in Volume Viewer) and specify a smaller size in this command.  But using a command is a pretty difficult approach to cropping the volume, more commonly it would be done interactively with the mouse using the Volume Viewer menu Features / Subregion Selection.



> On Feb 4, 2019, at 2:04 PM, Mauser, Jonathon  wrote:
> Thank you, Tom. What commands would I need to simply reduce the size of a density/surface model bounding box?
> From: Tom Goddard
> Sent: Monday, February 4, 2019 3:52 PM
> To: Mauser, Jonathon 
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: Re: [Chimera-users] Slicing/Subdividing Models in Chimera
> Hi Jon,
>   You won’t be able to get STL of a clipped molecule from Chimera — as you observed you get the full molecule instead.  The problem is that clip planes are just a graphical operation where the graphics decides not to display some of the pixels that would be behind or in front of a clip plane.  But the STL format is a list of triangles.  To make a list of triangles all the triangles cut by the clipping plane would have to be trimmed and the out of view triangles and partial triangles thrown away.  Chimera does not do that.  Often that is not enough as 3D printer software often requires the triangles are joined at their edges to form a closed mesh, and the tiniest gap causes the 3d printer software to fail (observed with old Catalyst software and uPrint printers).  Clipping and getting closed triangles requires even fancier software — this is typical of mechanical engineering CAD software.
>   The one thing you can do to slice is and 3D print is use a surface calculated from a density map, and reduce the bounding box of the density map.  The Chimera molmap command makes such density maps from molecules.  But it won’t give ribbon or ball-and-stick type appearances.
>   Lastly when cutting molecules you are likely to produce many disconnected fragments which will simply fall apart if you try to 3D print them after you dissolve the support material.
>               Tom
> On Feb 4, 2019, at 8:38 AM, Mauser, Jonathon wrote:
> Hello,
> I am working on developing a new suite of flexible multimedia 3D printed protein models using Chimera to process to .stl. I am trying to make a sort of “anatomical” cutaway of an enzyme complex where I can slice the model in chimera along a certain plane and print the sections with caps, but am running into problems. 
> I have tried simply clipping into the model, which does essentially what I would like to do, but I don’t know how to delete everything that I’ve clipped out of the model. When I export my scene, it still exports the whole model instead of the clipped depiction. Ideally, I would like to just cut the pdb in half to start with more advanced cutaways coming later. Do you have any idea how this might be accomplished?
> Thank you!
> Jon
> Jonathon Mauser, Ph.D.
> Assistant Professor
> Department of Chemistry
> Winona State University
> Office: Pasteur Hall 330
> P: 507-457-5874
> E: jmauser at winona.edu <mailto:jmauser at winona.edu>
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