[chimerax-users] Fwd: Troubles when saving a map

[Tom Goddard]

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
>> 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210618/367994ec/attachment-0001.html>