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

Elaine Meng meng at cgl.ucsf.edu
Sat Jun 19 08:54:43 PDT 2021

You can save maps with the "volume" command save options.  

However, map files do not contain rotation information, so they are not saved in transformed coordinates.  This is a commonly asked question, and is discussed here:
"Saving maps after fitting" section at the bottom of this page

Instead, to make a map and atomic structure match up, you may need to save the atomic model as a PDB file "relative to" the map model. There are "relative to" options in the File... Save PDB dialog and in the "write" command.


> On Jun 19, 2021, at 8:28 AM, Ritwik Jain via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 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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