Labeling 3D structures in Chimera (and saving them as such)
Hello, I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research. However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format? Thank you for your time and consideration. Any insight would be greatly appreciated. Bilal Asif Stony Brook University
Hi Bilal, We're happy to hear you might use Chimera in your lab! As you have seen, the usual "atomic structure" formats (PDB, mol2, etc.) only describe the atomic positions and do not include labels, display styles, colors, etc. However, different graphics programs including Chimera provide ways of saving all that information too. I assume you want a 3D structure that can be manipulated by the students, as opposed to a 2D image. (You could just use File... Save Image if you only wanted a picture.) Possibilities in Chimera: (1) The simplest is to save a Chimera session file, which can be done with the File menu or the command "save" -- later opening that file will restore the session. Disadvantages are that the file may be largish, and its contents are not meant for viewing in a text editor (it is Python code including all the structure and display data). Information on sessions: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> (2) Create a Chimera command file that does the coloring, labeling, etc. Just opening the command file (a plain text file named *.com or *.cmd) in Chimera will execute the commands. The command file could also open the structure. Example command file contents: open 2gbp preset apply int 1 ~disp solvent align ligand protein focus ligand z<3 rlabel :152,183 In that example, the structure 2gbp is fetched from the PDB, but you could also give a local file including its location. Or, the students could be told to open the PDB file and then the command file (which in that case would not include the opening step). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> (3) Fancier packaging of such a command file. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#command> Namely, starting with the same Chimera commands, one could: (A) create a Demo in Chimera (there are a couple of examples to play back in the Tools... Demos menu) <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html> (B) create a Chimera "Web data" file; clicking a link to such a file then calls the locally downloaded Chimera as a helper application. Also requires minor setup by webmaster. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/webdata/chimerax.ht...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 6, 2011, at 9:24 AM, Bilal Asif wrote:
Hello, I am a senior undergraduate student at Stony Brook University, part of a team currently attempting to design an introductory biology lab for biology undergraduates. We are attempting to use Chimera as a way to introduce students to structural biology and research.
However, we have run into a problem, one which we hope you can help us solve. We have discovered that if one attaches a label to a molecule in Chimera, one cannot save it as a .pdb, and open it again with the same labels attached. Is there a way to preserve labels attached to 3D structures, perhaps by saving it in a different file format?
Thank you for your time and consideration. Any insight would be greatly appreciated. Bilal Asif Stony Brook University
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
Hi Bilal, The Chimera sessions are in a format specific to Chimera, and are not used by other programs or for printing. However, Chimera can save several formats used by other programs, including STL and VRML; see File... Export Scene in the Chimera menu. You would probably want to save a Chimera session (so you can easily get back to the same state in Chimera) as well as exporting to one of these formats. These other formats don't include everything shown in Chimera, and only the VRML can be read back into Chimera anyway (and then you would have less information than the original molecular data). For example, STL does not include color, dots, lines, or text. A little more about exporting scenes: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/export.html> Our lab does have some experience with using STL files for solid printing in one color, but I am not the expert on that. We have a page about it here: <http://www.rbvi.ucsf.edu/Outreach/technotes/uprint.html> and perhaps some of the other lab members may chime in if they think there is more to say. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 8, 2011, at 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
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@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
_______________________________________________ Chimera-users mailing listChimera-users@cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Bilal Asif
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 <mailto: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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Bilal Asif
participants (3)
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Bilal Asif -
Elaine Meng -
Greg Couch