[Chimera-users] Question regarding the chimera Transform Coordinates feature

[Ritwik Jain]

Is there a command similar to write for saving EM maps because write is not
available for them. Actually I want to use molmap to create a simulated
chain of a protein which does not align to its original position. I tried
"volume #0.1 save emmap.mrc" but it does not work because when I reopen the
map it is aligned to its original position.

On Sat, Jun 19, 2021 at 2:01 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Ritwik Jain,
> Not sure I understand your question, but I'm guessing you just want to
> save the atomic structure with transformed coordinates?  If you move the
> atomic structure by any method (by hand with the mouse, commands like
> "move" and "turn" or fitting like "match" and "matchmaker") then you can
> save the transformed coordinates to a PDB file simply by using the "write"
> command.  By default, it will write the transformed coordinates unless you
> also used the "relative" option.
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
>
> If you have only one atomic model open, you can also do it by  un-checking
> "Use untransformed coordinates" in the Save PDB dialog (e.g. opened from
> File menu).
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 18, 2021, at 1:15 PM, Ritwik Jain via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Respected developers of chimera,
> > I am currently doing a research project related to Cryo-EM map alignment
> in which I need to use Chimera. Chimera has a feature which transforms the
> coordinates of a molecule (Img1.jpg) . That feature has an option to move
> atoms instead of coordinate axes (Img2.jpg). If I uncheck that box and
> transform, the model just reverts back to its original position after
> saving and reopening. I was wondering if there was a command line command
> for the " move atoms instead of coordinate axes " option. I have tried all
> the move commands (
> https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/move.html)
> and they don't seem to work.
> >
> > I expect your reply soon.
> >
> > Sincerely,
> > Ritwik Jain
>
>
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