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
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@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@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Hi, Stéphane, The pixel size is just a value in the header of the MRC file, and you can change it with Relion: relion_image_handler --i input.mrc --o output.mrc --force_header_angpix [new_value] Best wishes, Vadim Kotov Postdoctoral fellow, Löw group EMBL Hamburg 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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Stéphane ROCHE -
Tom Goddard -
Vadim Kotov