[Chimera-users] Flipping the map - resolution question

[Elaine Meng]

The only way to save a map with rotation (and have it "remember" the rotation) is to resample, since the map headers do not have rotation information in them.  This is discussed in the bottom section of this page:

<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfitting>

However, it will be obvious when you are resampling.  It is only when you use "vop resample" or specify the "onGrid" option of other vop commands, and the help for each of those commands links to the note on resolution.  The help for other commands that do not affect resolution do not link to that note.

Elaine

> On Jul 14, 2021, at 8:08 AM, Dmitry Semchonok via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Elaine,
> 
> Do you mean if I move the map and then save with the new coordinates?
> 
> 
> Thank you
> 
> Sincerely,
> Dmitry
> 
> 
>> On 14. Jul 2021, at 16:47, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Dmitry,
>> Saving a map to a file does not change its resolution.  The resolution note is only about when you resample the map to a different grid (different location of points) since that uses interpolation from the original points.
>> Best,
>> Elaine
>> 
>>> On Jul 14, 2021, at 4:41 AM, Dmitry Semchonok via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Dear Elaine,
>>> 
>>> Sorry for additional question but I am very curious - 
>>> 
>>> do I understand correctly that even the saving of the map volume (also the flipped one) in mrc volume also does not change the resolution of it?
>>> 
>>> 
>>> 
>>> Thank you!
>>> 
>>> Sincerely,
>>> Dmitry
>>> 
>>> 
>>> 
>>>> On 9. Jul 2021, at 16:57, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>>> 
>>>> Dear Dmitry,
>>>> No, "vop zflip" does not change the resolution.
>>>> 
>>>> Resampling on different grid points (vop resample) will decrease resolution.  However, "vop zflip" is not resampling, just reversing the order of the data planes.  The "vop resample" description links to that note about resampling and decreased resolution, but the "vop zflip" description does not.
>>>> 
>>>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
>>>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zFlip>
>>>> 
>>>> (You may be interested to know that ChimeraX can also flip, command "volume flip"
>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#flip>  )
>>>> 
>>>> I hope this helps,
>>>> Elaine
>>>> -----
>>>> Elaine C. Meng, Ph.D.                       
>>>> UCSF Chimera(X) team
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>>> On Jul 9, 2021, at 1:42 AM, Dmitry Semchonok via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>>>> 
>>>>> Dear colleagues,
>>>>> I heard that flipping the map in Chimera with the command 
>>>>> 
>>>>> vop zflip #
>>>>> 
>>>>> will decrease the resolution of the map
>>>>> 
>>>>> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#notes
>>>>> 
>>>>> Did I understand that statement correctly? 
>>>>> 
>>>>> If yes, how to flip the map without losing the quality (resolution)?
>>>>> Thank you
>>>>> Sincerely,
>>>>> Dmitry