Chimera does not have an analogous algorithm.  If you could send me a reference, it might not be hard to write a small script.  For instance, adding hydrogen bonds for strands will help stability and the Chimera commands to do that would be:

    select strand
    findhbond selRestrict strand

or with the menus:

    Select / secondardary structure / strand
    Tools / Structure Analysis / FindHBond
        Only find H-bonds with both ends selected
        OK

    HTH,

    Greg

On 04/08/2011 11:03 AM, Bilal Asif wrote:
Thanks.

In regards to adding fake bonds...I know Jmol has an algorithm for struts that allows stability in manipulated proteins. Does Chimera have an analogous algorithm to provide support for unstable structures? 

On Fri, Apr 8, 2011 at 1:44 PM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
For a ZCorp printer that has the ZPrint software, I'd recommend exporting VRML files from Chimera.  The advantage of VRML over STL is that VRML includes the color information and that Chimera is not as good as ZPrint at decimating spheres and cylinders into appropriate sized triangles for 3D printing.  Use the File / Export Scene dialog to export VRML files from chimera or use the export command.  And be aware that the cylinders used for bonds might need to be thickened so they don't break.  And you might need to add fake bonds to make the structure physically stable.

    HTH,

    Greg


On 04/08/2011 10:16 AM, Bilal Asif wrote:
Hi Elaine,

Thank you for such a comprehensive email! 

We had some follow up questions, however, which we were hoping you would be able to answer. We are attempting to use Chimera to model proteins, and then print them using a 3D printer (ZCorp software). The following file types are compatible with the printer software:

STL
VRML
3DS
ZPR
PLY

Can Chimera save in any of these formats, that can be used to print proteins? How would one save the session as one of these? Additionally, I had a question about saving the session in Chimera, to preserve labels and colored atoms. Is such a saved session a Chimera-specific file, where it cannot be read by external programs?

Thank you for your time. 

Bilal Asif
Stony Brook University, NY

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--
Bilal Asif