[Chimera-users] copy/combine molecular models

Rui Chen rchen6 at ualberta.ca
Thu Aug 22 10:01:33 PDT 2019

Dear Elaine,

Thank you so much for your help.

Best regards,

On Thu, Aug 22, 2019 at 10:33 AM Elaine Meng <meng at 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 at 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
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