Stephane's problem with the MRC map written by ChimeraX looking like noise in Coot was because the map origin was not correct. Tom

Begin forwarded message:

From: Stéphane ROCHE Subject: RE: [chimerax-users] Troubles when saving a map Date: June 18, 2021 at 5:37:12 AM PDT To: "Vadim Kotov" , "Tom Goddard"

Thanks to both of you for your help !

I have finally understood what was happening, the origin of my map was changed and it was a very long way from its old position given that the box was quite large. So basically, when if I was looking around for densities, I was only scrolling inside the solvent.

Thanks again, Stephane Roche

On 17.06.21 10:07, Stéphane ROCHE via ChimeraX-users wrote:

...

Dear Mr/Mrs,

I am new to ChimeraX (v 0.7) and I have a trouble when saving a map.

I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. - Opening the map is fine. - Then I change the pixel voxelsize which is also fine. - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created

Do you know what I could do to solve this problem ?

Thanks, Stephane Roche Institut de Biologie Intégrative de la Cellule 91198 Gif sur Yvette France