[chimera-dev] Help with chimera extension for 3D printing

[Stephen Norris]

Hello Tom,

First of all, my comment about the units in chimera being arbitrary was in
respect to how they are useless without knowing the corresponding scale
that the model will be printed at. This is a problem for us because as I
mentioned we don't really have a good method currently of determining the
scale we want to print at in chimera and then transferring that scale to
the printer software. Additionally it is difficult to compare sizes for
printing as we need to have both a saved build file from the printing
software and an original chimera session. This is because both the scale of
printing and original settings used in chimera affect the actual size when
printed. What we can do however is pick up a pair of calipers and actually
measure the width of segments of models we've printed.

Also, I should be clear and try to explain what the extension currently
does as it may clear things up. The extension uses the monitor's physical
dimensions/DPI, which it tries to automatically get using the Tk winfo
commands as you mentioned. I've found that the DPI isn't actually reported
on some systems such as ubuntu (The X11 developers are at fault for that
but don't get me started) so there is an option to manually determine these
parameters. The extension can then use the horizontal dpi to determine the
physical width of the viewer window and use set the view size to be the
actual physical size (in inches).  This then means the viewer's scalefactor
is then the printing scale factor to get a model the same size as what is
displayed on the screen (in inches, but can be converted easily).  In
addition there is a grid and ruler system so if you wanted a model 10cm
across you can turn on the grid and simply zoom the model so that it fits
into 10cm.

So, for exporting the model it would be good to have the scaling built into
the export. Your point about surfaces is good, for that side point I was
only thinking about simple ball and stick kind of stuff but that idea
doesn't really pan out when it comes to making it work for everything else.
The main working idea I have though is to modify the x3d export so that all
the models are placed under a single transform node that holds the printing
scaling. This can be done by simply nesting it just inside the group tag.
>From what I can tell this works fine even with the x3d2vrml conversion
program with a test x3d file I modified by hand.

For setting style parameters the idea is that the extension can use the
current scalefactor to determine the size in angstroms to set each
parameter. So if we wanted struts of diameter 3mm and the model was
currently at 50% scale, the extension can convert 3mm to inches and then
divide by the scale to get struts of 3mm. What would be great would be to
be able to set them to be 3mm but have them update to stay 3mm when the
scale factor changes. This could be done by setting every parameter every
time the scale factor changes but I'm guessing this would be too expensive
to work in real time smoothly.

Stephen

On Tue, Jul 19, 2016 at 7:34 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Stephen,
>
>   Your printed molecular models are neat and your Chimera extensions is
> interesting too.  Here are some ideas on what is possible in Chimera
> regarding size scale.
>
>   First the Chimera units are not arbitrary, they are Angstroms because
> all molecular structures are in Angstroms.  Chimera uses certain atom
> sphere sizes and ribbon thicknesses, and those are all assuming the units
> are Angstroms.  If you have a protein that is say 50 Angstroms across and
> you want to print it as a plastic model 10 cm across you would end up using
> a scale factor of 0.2 in the printer software to convert from the Angstroms
> in the Chimera exported STL or X3D or VRML or OBJ file to centimeters, and
> you would tell your printer software to use centimeters.  When I am
> designing a molecule model to print I first decide how big I am going to
> print it, e.g. 10 centimeters.  I know the smallest feature my printer can
> make that won’t break to easily is say 0.2 centimeters which is 50x smaller
> than my model size.  So I need to make all features at least 1/50 of the
> full size, or 1 Angstrom for a 50 Angstrom model.  When making models to
> print I usually decide the smallest features can only be 1/50 the full
> size, then I choose strut radius and ribbon thickness by eye so they appear
> at least 1/50 the full molecule size.
>
>   This could all be simpler if all the sizes in Chimera like strut radius
> or ribbon size was in centimeters and you already scaled your molecule up
> to be 10 centimeters across.  I don’t advise trying to do that.  You could
> after you open a PDB molecule file use some Python code to scale all the
> coordinates, atom radii, bond radii, ribbon thicknesses.  But you will
> create problems because many Chimera tools assume Angstroms.  For instance
> if you make a molecular surface it is going to use a probe radius of 1.4
> Angstroms for computing the surface and this may be very bad for the scaled
> model.  If you ask for hydrogen bonds it will use expected hydrogen bond
> lengths in Angstroms, and simply won’t work.
>
>   So instead I think you should live with the fact that Chimera units are
> Angstroms, and the exported X3D, STL, … is in units of Angstroms, and
> instead try to help provide scale factors and suggested minimal feature
> sizes.  I don’t know of any way to scale the coordinates in the X3D or STL
> produced by Chimera other than changing all the molecule dimensions.  So I
> guess I’d suggest your extension should help them determine the model size
> to print, maybe by reporting the current size as shown on screen.  For that
> you should really use the actual screen DPI, not 72 — the Tk "winfo pixels”
> command should give you that.  Then you might report a scale factor from
> Angstroms to the displayed physical size on screen in centimeters (for
> entering to the printer software).  And maybe you could also report the
> displayed physical ribbon thickness and strut diameter (in centimeters).
>
> Tom
>
>
> On Jul 19, 2016, at 8:48 AM, Stephen Norris wrote:
>
> Hello Chimera developers! I'm a recent graduate of URI where I worked as
> part of a 3D printing group working on molecular visualization. You can see
> some examples of our work at http://web.uri.edu/pharmacy/3d/3d-gallery/ .
> When we started the program we used both Jmol and Chimera on individual
> models but ever since Tom added the struts commands we've been 100% using
> Chimera and loving it! However as I'm ending my personal involvement in
> projects there, I still want to do one last thing which is to solve a major
> headache for the 3D printing process.
>    When developing model in Chimera we cannot really determine what scale
> the model and it's components like strut diameter will be when printing.
> These scales can only really be determined once we import the model into
> the 3D printing software and set an overall scaling for the model. This is
> a problem as we can easily make a model which looks nice but when we
> determine the overall scale the struts may turn out to be too thin, and
> then we have to go back and re-export the model until we get them
> acceptable. In addition is no way to relate the scale of a model shown in
> the viewing window to an actual scale we could input to the computer
> software.
>    The solution would be to have functionality in Chimera to work with the
> model and scale things in terms of real-life units. A program like
> solidworks would easily let one do this but for Chimera units are somewhat
> arbitrary. One trick with the 3D printing software is that the print bed is
> shown with a grid of units so we can expand the ortho view until the screen
> is showing the objects to be printed at their actual real life sizes. I've
> already developed an extension to do this in Chimera and a side effect is
> that the scale to input to the printer to get a model at the scale
> displayed on the screen is easily obtained. I've made a github repo for the
> extension at https://github.com/gerbi7/UCSF-Chimera-RealScale-Extension .
>    So now I'm running into two problems which could use some expert advice
> or ideas:
> 1. It would be good to be able to export models with the scaling
> pre-applied so that one just has to select the correct unit when importing
> to the 3D printing software. As far as I can tell most of the export
> functionality is in C++ and doesn't include support for applying a global
> scale to an export. Since it's in C++ I don't know if this would be viable
> as an extension to modify it. So far my idea would be to modify the
> outputted file?
> 2. It would be incredibly useful if one could set style parameters such as
> ribbon width, strut widths, etc in terms of real-life units, and have them
> stay constant while the user can modify the overall scale of the model by
> zooming in and out. It would be good if there was some elegant way of doing
> this instead of brute-force setting every parameter whenever the zoom
> changes.
> As a side note if it was possible to just insert a scaling factor whenever
> an atom coordinate is needed for graphics purposes that would probably work
> to solve both problems but I doubt that exists currently.
>    I look forward to hearing back from you.
>        Stephen Norris
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