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
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Tom Goddard