[Chimera-users] saving rotated volume

[Reginald McNulty]

Hi Elaine,

It works!

There’s just one issue. My original volume was in PIF format – there are two contours that can be manipulated for the single volume. When I saved the final file and reopened it, it is aligned to the Z-axis, but the visible density is on the wrong side of the contour. That is, density outlining the protein was saved. Once I track down how to prevent this, the procedure you outline works fine. I suppose if one starts with a proper MRC file, then everything would work fine.

Reggie

> On May 18, 2017, at 6:34 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> P.S. “vop new” is a relatively recent addition, so you would need to have Chimera version 1.11 or newer to use that command
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.11.html>
> 
> 
>> On May 18, 2017, at 3:30 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Reggie,
>> Ah, this is a frequently asked question… the issue is that map files do not include the rotation information.  If you had fit to another map, the solution would be to resample the rotated map on the grid of the other, as described here:
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>
>> 
>> Hmmm, I haven’t tried this myself, but one idea is to make a new zero-valued map “vop new” and then resample your rotated map on the grid of that zero-valued map.  If you were careful to rotate only your virus map, then the new dummy map would still be aligned with the displayed axes.  However, you’d have to create the new map so that it encloses your existing rotated map (show box outlines with Volume Viewer).
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
>> 
>> There may be a more intelligent approach, but that’s all I can think of currently.  I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On May 18, 2017, at 12:19 PM, Reginald McNulty <rmcnulty at scripps.edu> wrote:
>>> 
>>> Dear Users,
>>> 
>>> I have two objects open in Chimera. One is a .bild file that shows axes x,y,z. The other is a volume of a virus with a tail. I used “activate only” to manipulate the volume relative to the axis.bild object. After rotating the virus to align the tail to the Z-axis, I try to save the map but it’s always back in the original position when I re-open it in Chimera. Is there a way to save this transformed map?
>>> 
>>> -Reggie
>>> 
>> 
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>