Dear Elaine, Thank you so much for your help. Best regards, Rui On Thu, Aug 22, 2019 at 10:33 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Rui, Maybe you mean you want to save a PDB file? (there is no pub file). After you make the new model, then use menu: File… Save PDB <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
The answers to all of these questions are: it depends what you want. The options do exactly what they say they do… clicking the Help button shows the explanations: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine>
I’m guessing, however, that you can just use the default settings in the dialog if your purpose is just to get a PDB file of the homodimer model.
The structure will be the same structure no matter which reference coordinates you use, it just might be located differently in space (translated or rotated overall).
Model ID is not saved in the file, it’s just an ID for the new model when you create it in Chimera. Just use a model ID number that is not already used by some other model (you can check this using menu: Favorites… Model Panel). Then later in the Save PDB dialog, that is the model to save.
The rename/retain options are because the two chains might have the same residue numbers as each other and you need to some way to tell residues apart in the new model. The two choices are (1) rename chains (i.e. you might get chains A and B) but keep numbering or (2) change numbering. I personally prefer (1) because it’s easier for me to specify later actions on that model like coloring a specific residue or chain, but it may not matter to you.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 21, 2019, at 11:07 PM, Rui Chen <rchen6@ualberta.ca> wrote:
Hello, I am working on a homodimer. I modelled loops of each chain one by one. I chose the best loops for each chain. Now I want to save them as a pub file. Please see the following screenshot. How to decide the new model's ID? I know the coordinate system is the reference coordinate, how do I decide which chain to use as the reference chain? Should I choose rename them uniquely? Looking forward to hearing from you. Thank you. <Screen Shot 2019-08-22 at 12.01.28 AM.png> Best regards, Rui