[Chimera-users] Fwd: STL Output

[Tom Goddard]

Begin forwarded message:

> From: Tom Goddard 
> Subject: Re: [Chimera-users] STL Output
> Date: June 10, 2014 at 2:02:27 PM PDT
> To: Eric Bell <Eric.Bell at oberlin.edu>
> 
> Hi Eric,
> 
>   Chimera doesn’t represent molecules as polyhedrons.  Are the orange octahedrons each representing one molecule?  And what are the red spheres at the corners, with some red spheres out in space?  And what are the little attached pink spheres?  This kind of display would require a new Chimera plug-in.  The graphics would be easy to do in Chimera.  I don’t think such a model would hold together very well when printed in 3d.
> 
>   The Crystal Contacts tool in Chimera is remotely related, showing contacts between asymmetric units in a crystal
> 
> 	https://www.cgl.ucsf.edu/chimera/experimental/crystal_contacts/clashes.html
> 
>   Tom
> 
> 
> On Jun 10, 2014, at 1:50 PM, Eric Bell  wrote:
> 
>> Dear Tom,
>> 
>> The polyhedral models look something like the attached image.  Does chimera do anything like this or would I have to code a separate plugin?
>> 
>> Thanks,
>> Eric<polyhedra.jpg>
>> On Jun 10, 2014, at 2:15 PM, Tom Goddard  wrote:
>> 
>>> Hi Eric,
>>> 
>>>   Not sure what kind of CrystalMaker polyhedral models you were thinking about printing.  Chimera can show crystal unit cells.  Here are 4 unit cells each containing 8 copies of a small protein (1a0m) shown with the Chimera Unit Cell tool (menu Tools / Higher Order Structure / Unit Cell) with the proteins shown as solvent excluded surfaces (menu Actions / Surface) and each unit cell colored differently (selected by hand with a mouse drag, then used menu Actions / Color).
>>> 
>>> 	Tom
>>> 
>>> <1a0m_2x2_unitcells.jpg>
>>> 
>>> 
>>> On Jun 8, 2014, at 7:47 PM, Eric Bell wrote:
>>> 
>>>> Dear Chimera Developers,
>>>> 
>>>> My name is Eric Bell, and I am a student at Oberlin College.  I have been using Chimera for 3d printing of molecular models because of its ability to handle many of the processes needed for atom editing as well as its ability to export in an .stl format.  However, an issue I've run into is that the resolution of those .stl meshes is rather high, and there does not exist an option, to my knowledge, to alter the amount of vertices on the spheres.  This causes an issue when we want to print spacefill models of large molecules, because Chimera will output such large files that our software isn't able to properly process the file without serious resource consumption.  Is there anything that I as a user can alter to change the resolution of these spheres, or is it a setting that has been compiled so that I can't edit it without recompiling?  I am familiar with python so navigating code would not be an issue for me if necessary.  Thank you!
>>>> 
>>>> Sincerely,
>>>> Eric Bell
>>>> 
>>>> P.S. Another thing we were looking for that has yet to be done is to print polyhedral models like those in programs such as CrystalMaker.  As far as I know Chimera doesn't have this functionality but a programming environment called Bsoft is using the native save file format of chimera to do it because of its similarity to XML.
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>>>> 
>>> 
>> 
> 

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