[Chimera-users] Labeling 3D structures in Chimera (and saving them as such)
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:
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:
> 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.
> 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:
>> 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>
> Bilal Asif
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