[Chimera-users] default position in space

Tom Goddard goddard at sonic.net
Mon Mar 7 10:26:55 PST 2016

Hi Jakob,

  With the 3d printer software we use (Catalyst) a key step to set up the print job is to position and scale the model in the printable region.  I’m surprised if the print software you use does not allow that.

  But here are details to understand the coordinates you get using File / Export Scene… in Chimera.  When you open a PDB model the atom coordinates are in crystallographic coordinate frame — it could be centered anywhere and oriented any way depending on how it is positioned in the crystal.  The units are always in Angstroms.  If you use Chimera Export Scene after opening a PDB model without moving it, then you get exactly those crystallographic coordinates.  If you rotate the model with the mouse before exporting then it will be rotated in the STL output.  To get it back to the initial orientation in Chimera use the “reset” command (menu Favorites / Command Line).

  Chimera doesn’t have a simple way to position in absolute coordinates nor scale the coordinates since these are rarely needed.  But here is an idea if you need to do that.  First make a low resolution (5 A) density map from the PDB model

	molmap #0 5 grid 1 modelId #1

That map will align with the PDB.  But we can change that so one corner is at the 0,0,0 origin and show an outline box around it using command

	volume #1 origin 0,0,0 showOutline true

Now it won’t align with the PDB model but you can see how the PDB model is positioned in this box.  Then you could move the PDB with some other commands (e.g. "move y 15 model #0" or "turn z 20 model #0”), or with the mouse by freezing the motion of the map using Model Panel (Favorites menu) and clicking the Active button (“A” column) off for the map.  When you export STL hide the map using the Model Panel show button so it is not included in the output.


> On Mar 7, 2016, at 2:39 AM, Jakob Suckale wrote:
> Dear Chimera team,
> What determines the position of objects in space?
> I have done some testing with tubulin (1TUB), hemoglobin (1HHO), and
> collagen (1BKV). They all end up in very different and seemingly
> random position in print space after STL export (see screenshot).
> Is there a way to predict how items will appear to allow one to adjust
> the position beforehand with move commands?
> This is secondary for in silico simulations within Chimera but crucial
> for printing of real models. If they are cut by the plane everything
> below will not be printed, i.e. tubulin in my example would not be
> printed at all without adjustments and the others would be cut.
> All the best,
> Jakob
> <default model position.jpg>_______________________________________________
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