[chimerax-users] Troubles when saving a map

[Tom Goddard]

Hi Stephane,

I am not sure why your map saved by ChimeraX looks like noise in Phenix and Coot.  ChimeraX writes MRC format which is almost identical to CCP4 format.  They differ in how the map origin is specified using different header fields but ChimeraX writes reasonable origins for both ways of specifying the origin.  My only guess is that there is a flag indicating endianness -- the order of the 4 bytes in a floating point value, and somehow that is backwards so all the floating point values are misread.  What operating system and what CPU does the machine use that wrote the file?  And what is OS and CPU when reading the file?

If you use ChimeraX menu Help / Report a Bug... and attach the map file I can look at it.

ChimeraX 0.7 is ancient -- the current version is 1.2.  But I don't think writing MRC files has changed.

	Tom


> On Jun 17, 2021, at 1:07 AM, Stéphane ROCHE via ChimeraX-users <chimerax-users at cgl.ucsf.edu> 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
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20210617/0bdbe19a/attachment.html>