[Chimera-users] Question regarding saving PDB in Chimera
meng at cgl.ucsf.edu
Mon Jan 5 14:28:59 PST 2009
If you just want the transformed coordinates (as shown on the
screen), don't check any options. That is, don't use "save relative
to" some model. However, that only saves the atomic structure and
not the map, so if you had rotated the entire view you would lose
their relationship and the fitting. I believe you want to save the
atomic model relative to the density map model.
To save the original coordinates of a model, you would "save relative
to" itself, for example, save model #0 relative to model #0.
Normally that would be done if you did something like rotated a bond
or added hydrogens but otherwise wanted the same coordinates as
input. Another use is if you superimposed or docked #0 and #1 and
wanted to save their relative orientations. In that case you could
either save #1 relative to #0 (so that the saved #1 would work with
the original file for #0) or vice versa, assuming both are atomic
In your case, with a density map and an atomic structure, you can
only save the atomic structure as PDB, of course.
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Jan 5, 2009, at 11:13 AM, Pancera, Marie (NIH/VRC) [E] wrote:
> I am using Chimera to fit coordinates into EM density.
> However I have problems when I save with Chimera as the coordinates
> that I am saving are not the one I see on the screen.
> Here is what I do:
> Save PDB
> chose the folder
> A file name
> A file type
> The model that I want to save, i.e the one I see on the screen
> And then I have to select save relative to model, otherwise I am
> saving the original molecule, the problem is that I am not sure
> relative to which model I have to save it.
> IS there an easier way to just save what I can see on the screen?
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