[chimerax-users] Fit crystal structure into mrc

[SHIQING LIAO]

Thank you so much for your help! It worked!

Best,
Shiqing

On Tue, Jun 29, 2021 at 5:30 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Shiqing,
>
> If you want to scale your marker positions you can do it with a bit of
> Python typed in the ChimeraX Python shell, menu Tools / General / Shell.  I
> selected my markers "select #2" then scaled their coordinates by a factor
> of 1.5 with
>
> from chimerax.markers import selected_markers
> m = selected_markers(session)
> m.coords = 1.5 * m.coords
>
>   Tom
>
>
> > On Jun 29, 2021, at 5:06 PM, Elaine Meng via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hi Shiqing,
> > Sorry no, there are no "voxels" in an atomic structure.  The scale of an
> atomic structure is well established, with bond lengths and distances in
> Angstroms.  So whenever there is a scale mismatch between atomic structure
> and map, it's essentially always the map model that needs a different voxel
> size.  Markers are implemented as atomic structures, so even though they
> aren't "real" atoms, there is no built-in function to change their scale.
> >
> > If you color the map before you change its voxel size, do you still need
> the markers?
> >
> > If so, you would probably need to write your own script to calculate new
> marker coordinates to match the new map dimensions, or simply start over
> with adding the markers to the map after you change its (the map's) voxel
> size.
> >
> > I hope this makes sense.  Sorry for the difficulties,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Jun 29, 2021, at 4:42 PM, SHIQING LIAO via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >>
> >> Hi,
> >>
> >> I am trying to build an illustration using marker/color zone. I
> successfully colored my mrc file. Now, I want to fit a crystal structure I
> downloaded from pdb into the mrc. But they apparently have different sizes.
> I tried voxelSize to scale up my mrc, but then all my markers don’t fit
> with the enlarged mrc. However, voxelSize doesn’t seem to work with the
> crystal structure (.pdb1) as I got an error message “no volumes specified”
> when I indeed wrote “volume #5 voxelSize 2”. I am wondering is there any
> function like voxelSize to scale down the crystal structure? Thank you!
> >
> >
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> >
>
>
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