[Chimera-users] 3D printing a viral capsid

Tom Goddard goddard at sonic.net
Fri Aug 22 14:57:28 PDT 2014


Hi Jeremiah,

  The symmetry for your capsid is 222r, not 222.  These both have 2-fold symmetry axes along x,y,z but they differ by a rotation by 90 degrees about z which puts the 5-fold symmetry axes in different locations.  To figure out the right simmetry I used the Chimera Icosahedron Surface dialog (menu Tools / Higher-Order Structure) to show an icosahedral cage and then I try different standard orientations to find the one that matches.

	Tom




On Aug 22, 2014, at 2:31 PM, Jeremiah Gassensmith  wrote:

> Many thanks.  Using the OBJ did indeed work to get it into Blender (Freeware) to convert it to STL.
> 
> Related to Tom’s suggestion I tried (before I emailed the listserv):
>  
> >molmap #0 4 symmetry i,222
> 
> but I’m not sure why that didn’t work (that should be the right symmetry…?)  
> 
> molmap #0 4 sym biomt works, however.
> 
> 
> 
> Again, Many thanks.
> 
> Jeremiah
> 
> 
> On Aug 22, 2014, at 4:27 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
>> Here’s the molmap capsid image.
>> 
>> 	Tom
>> 
>> <capsid.jpg>
>> 
>> 
>> On Aug 22, 2014, at 2:25 PM, Tom Goddard <goddard at sonic.net> wrote:
>> 
>>> Hi Jeremiah,
>>> 
>>>  The STL export of your virus capsid multiscale model is giving just one asymmetric unit and that is a Chimera bug.  I’ll make a bug report and see if I can fix that.
>>> 
>>>  Here’s another suggestion about how to print it.  Make a single density map for the entire capsid with the Chimera molmap command
>>> 
>>> 	molmap #0 8 sym biomt 
>>> 
>>> This makes an 8 Angstrom resolution map using the asymmetric unit of the capsid PDB model #0 and uses the symmetry specified in the PDB file BIOMT remarks.  I’ve attached an image of what it looks like.  If you print on a single color printer this surface exported as STL is likely to work better than the Chimera Multiscale surfaces which may not be touching enough to hold together.  Also it gives a better (and very different) appearance because it is single color.  You can try different resolution values and see what works best.  The resolution of 3d printers isn’t too good, so having too much detail doesn’t produce the best printed model.
>>> 
>>> 	Tom
>>> 
>>> 
>>> On Aug 22, 2014, at 10:33 AM, Hurt, Darrell (NIH/NIAID) [E]  wrote:
>>> 
>>>> Hi Jeremiah,
>>>> 
>>>> I got a good import of your scene in Blender by exporting an OBJ from Chimera. Maybe give that a try. You can then convert to STL using Blender's tools.
>>>> 
>>>> Hope it helps!
>>>> Darrell
>>>> 
>>>> 
>>>> From: Jeremiah Gassensmith 
>>>> Date: Friday, August 22, 2014 10:15 AM
>>>> To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
>>>> Subject: [Chimera-users] 3D printing a viral capsid
>>>> 
>>>> Hello
>>>> 
>>>> I’m trying to produce an STL file from a model I have built in Chimera but it comes out incredibly deformed.  I have created the model from a PDB file of a viral coat protein such that it is fully assembled into the proper capsid structure.  You can see the model I’ve created here:
>>>> 
>>>> https://dl.dropboxusercontent.com/u/9856122/CAPSID.py
>>>> 
>>>> Problem is, when I export to STL and open in Blender I get a squished unrecognizable “clump” looking thing and not a beautiful sphere.  Any help would be lovely!
>>>> 
>>>> Thanks!
>>>> Jeremiah
>>>> 
>>>> _______________________________________________
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
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>>>> 
>>> 
>> 
> 

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