[Chimera-users] 3D Printing our protein
Elaine Meng
meng at cgl.ucsf.edu
Mon May 20 15:37:52 PDT 2013
Hi Bart,
The Volume Viewer tool has so many features (many also available via the "volume" command) it would be difficult to summarize in a single tutorial. It depends what you are trying to do. However, there are several "how-tos" for specific tasks in this volume tour page:
<http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>
… and several tutorials that involve density maps and Volume Viewer in some way:
<http://www.cgl.ucsf.edu/chimera/tutorials.html>
<http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html>
There are also manual pages for Volume Viewer and related tools, although we certainly realize the learning curve can be steep because there is so much functionality. You can click the "Help" button on a tool to see its manual page, e.g. for Volume Viewer:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
... and use the command "help" to see the manual page for a command, e.g.:
help molmap
… which would show this:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>
In your example molmap command, the "selected" specifies which atoms to use, 3 is the resolution, and "grid 0.3" gives the spacing of grid points in the simulated density map. The command has several additional options.
No need to feel bad, there is just a lot of stuff in Chimera and it may take a while to learn what you need and how to use it!
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On May 20, 2013, at 3:00 PM, Bart Janssen <Bart.Janssen at plantandfood.co.nz> wrote:
> Hi All
>
> Thanks very much for the replies.
>
> Thank you Darrell for the model you made for us. I would still like to learn how to do it for myself though.
>
> Dr Swett - I had not realised I could save the domains as new .pdb files and then model them, I think that will work pretty well.
>
> Tom I had found those pages but they were pitched a bit above my Chimera skill level, however I did “just have a go” using those command lines for my protein and got a volume. After some trial and error I figured out how to use molmap to make a volume out of the selected domains and have been trying to figure out what all the various options in the volume viewer actually do (apart from completely crashing my computer because I made too many triangles of course). Is there a video tutorial for the volume viewer? I am still not certain exactly what I’m doing with the modifiers on the molmap command
> Molmap selected 3 grid 0.3
> Brings up something I can work with and export an .stl scene from (if I select the desired sequence from the sequence viewer) - but is the “3 grid 0.3” setting the grid spacing? And how will that affect the final .stl model. From my fiddling it seems the first number affects what I would call the resolution with which the volume map is generated, the smaller the number the closer the volume is to the actual individual atoms, bigger numbers create shapes that cover multiple atoms (possibly more “real”), is this number the “gridspacing”. The second number (0.3) seems to change the step in a way I just don’t understand, yes I can fiddle with the step to get a prettier image but I can’t figure out from the “adjust step” description what I am doing.
>
> I had a go changing the settings in the surface and mesh options of the volume viewer since they seemed to relate to how detailed the model would become but quickly discovered I could overload my computer :). Too many triangles appears to be a bad thing :).
>
> I have a strong sense that I am asking really stupid questions because I lack some basic understanding. Thanks again for all the help
>
> Cheers
> Bart
>
> From: chimera-users-bounces at cgl.ucsf.edu [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Tom Goddard
> Sent: Tuesday, 21 May 2013 5:57 a.m.
> To: R.J. Swett
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] 3D Printing our protein
>
> Hi Bart,
>
> Did you see the 3D printing page on the Chimera web site?
>
> http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html
>
> and
>
> http://www.cgl.ucsf.edu/Outreach/technotes/uprint.html
>
> Our usual approach to printing plastic models on our uPrint 3d printer is to use surfaces made with the molmap command. This simulates a density map for a molecule at any desired resolution. Then we export as an STL file which the printer software can handle. We make multi-piece models by creating a surface with molmap for each piece.
>
> We've encountered various problems using other approaches to print 3d models. My experience with this is a few years old so these problems may not exist now. One was that if you display atoms as spheres (or ball and stick) and try to print the model may come out as lots of pieces. It appears the printer software does not fill the regions that are inside an even number of surfaces. So if two spheres intersect, the intersection region is not filled with plastic. Ribbon display has worked for us but the models are fragile even in the strong PVC plastic we use. Also our printer software has a hard time with large STL files. I think the limit was a few hundred megabytes. That size can be controlled using the "gridSpacing" option to the Chimera molmap command.
>
> When printing multi-piece models a significant problem is that the pieces don't fit together because of clashes. For example and ball needs to fit into a socket but it is too big to be pushed through an aperture. Basically the interfaces are not convex and so steric clashes prevent placing them together. You can fix this problem by raising the contour level on the molmap surface (molmap produces a density map and isosurfaces from that density map) to shrink the surface a bit. If you want to get fancy you can use the mask command to chop away obstructions that would prevent the surfaces from fitting together.
>
> We have not had any luck printing using VRML or OBJ formats, only STL. But this would depend on your printer software. Those formats do export correctly from Chimera and can be viewed in other software. But they are more complex than the STL format, which is simply a list of triangles making up surfaces.
>
> Tom
>
>
> On May 20, 2013, at 6:02 AM, "R.J. Swett" wrote:
>
>
> You might want to try saving the two domains as separate PDB's if there are export issues with hidden domains. If you hide a domain and then go to save pdb and select "save displayed only" you'll be able to save each domain in it's own file. As far as file formats go, have you tried VRML? I know that's pretty universal for 3D printers and might help with studying the structure as you'd be able to color the atoms by their atom types. Is your 3D printer capable of color? Another thing you might want to try is displaying the protein backbone as ribbon and the sidechain as wire and setting the wire thickness to a higher number. That might give you the internal detail you want without saving the data for every single atom. Also, displaying as Ball and Stick might work too. Those controls are in the Actions > Atoms/bonds menu. Also, are you wanting to include the solvent or are you deleting it?
> R.J. Swett
> Wayne State University
> 357 Chemistry
> Detroit, MI 48201
>
> Lab Phone 313-577-0552
> Cell Phone 906-235-0768
> On 5/19/2013 9:23 PM, Bart Janssen wrote:
> Hi
>
> My apologies for what are likely to be stupid questions. We are plant developmental biologists and we just obtained our first X-ray crystal structure for a new hormone receptor in plants. We’d really like to make a 3D model of the protein using one of the 3D printers at our institute.
>
> I’ve been trying to use and understand Chimera for the last week and I’m a bit out of my depth :). I can import our protein 4DNP.pdb and display it using solid surface or using the sphere representations of atoms. I can also display it with the “lid” domain hidden and vice versa.
>
> My problem has been getting files that our 3D printer can read. The solid surface model of the whole protein can be exported as a scene in .stl format and that can be printed just fine. Although I can’t figure out how to adjust resolution or the smoothness of the exported file.
>
> But I’d really like to print the two domains of the protein separately. If I use Solid surface model with the lid hidden what I get is an eggshell like model which has no internal detail. If I use atoms shown as spheres instead I get the internal detail I want BUT when I try and export the scene I get a 2 Gb+ file that is unreadable by the printer. If I export .obj format instead the colleague who runs the printer says the file won’t load and appears to have errors.
>
> I have a horrible feeling I am going about this entirely the wrong way but I can’t find a tutorial that describes what I’m trying to achieve. I do realise chimera is not really written for the somewhat trivial use that I am attempting but it really would be helpful if we had a physical model of the protein to look at.
>
> Is there a tutorial I should follow or another part of Chimera (or another program) that I should be using instead? Any advice would be much appreciated.
>
> Cheers
> Bart
>
> Bart Janssen
> Scientist
> Plant Development team
> Breeding and genomics
> Plant and Food Research
> Private Bag 92169
> Auckland 1142
> New Zealand
>
> Ph +64 09 9257179
> bart.janssen at plantandfood.co.nz
>
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