[chimera-dev] Dust Clean in cryo-EM maps

[Elaine Meng]

Hi Amichai,
Hide Dust does not change the data, it only changes the appearance by hiding the small surfaces.  So as you saw, your saved map after hiding dust will be the same as before hiding dust.

<http://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/volumeviewer/hidedust.html>

However, as mentioned in the link above, you could mask out the dust areas  to create a new map, by 
(1) hiding dust
(2) showing ONLY the dust using command “sop invertShown”
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html#invertShown>
(3) using the “mask” command to make a new map with the dust areas zeroed
<http://www.rbvi.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html>

Another approach is to use Volume Eraser to manually “erase” (zero) parts of the map.
<http://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/voleraser/voleraser.html>

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 16, 2018, at 12:10 AM, ⁨עמיחי הולצר⁩ <⁨amiholz at gmail.com⁩> wrote:
> 
> Hi,
> I like the density map after hide density map, is there any way to save the density map after dust hide? Every time I save the density map, it saved the original map instead of density map after hidden dust.
> Thanks,
> Amichai
> 
> 2018-07-13 17:16 GMT+03:00 עמיחי הולצר <amiholz at gmail.com>:
> Chimera System Hi,
> I am a student in computational structural biology lab in the Hebrew University of Jerusalem. We are developing software for modelling with electron microscopy density maps. 
> I'm using chimera to display the density maps, and the specific using thr feature in chimera called clean dust, which shows the map seamlessly. 
> My question is whether there is a possibility to save the map without the "dust"?
> Because now there is only an option to eliminate dust, but not to save the clean map.
> Thank in advance,
> Amichai Hozler
> Hebrew University