[Chimera-users] Labeling 3D structures in Chimera (and saving them as such)

Greg Couch gregc at cgl.ucsf.edu
Fri Apr 8 13:47:25 PDT 2011

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



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 at cgl.ucsf.edu 
> <mailto:gregc at 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
>>     _______________________________________________
>>     Chimera-users mailing list
>>     Chimera-users at cgl.ucsf.edu  <mailto:Chimera-users at cgl.ucsf.edu>
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> -- 
> Bilal Asif

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