voxel size in mask.mrc header

[Bonnie Murphy]

Hi, This is a very small thing, but the masks we've created with Relion3-beta don't seem to have the correct voxel size in the header - regardless of voxel size of input model or input parameter in the gui, the mask (at least as viewed in Chimera) has a voxel size of 1. This doesn't seem to make any problems when using the mask in Relion, only when viewing it in an external program (and of course one can simply reset the value to see the mask properly overlaid on the volume). Cheers, Bonnie

[Takanori Nakane]

This is strange. On our system, the output from relion_mask_create has the correct pixel size in the header, confirmed by header command from IMOD and also by Chimera.

Are you using the latest version? How did you run it? Can you paste note.txt here?

Takanori Nakane

[Bonnie Murphy]

Hi Takanori, We last updated on Monday (30 July) and the job pasted below was run Tuesday (though this happened also with jobs run last week). Below is an example of the note.txt file that gave a mask with pixel size 1. I just ran it locally, launching from the gui. Best wishes, Bonnie

++++ Executing new job on Tue Jul 31 14:08:25 2018 ++++ with the following command(s): which relion_mask_create --i PostProcess/job288/lowpass15_postprocess_masked_noF1_formask_thresh0p018.mrc --o MaskCreate/job316/mask.mrc --ini_threshold 0.018 --extend_inimask 2 --width_soft_edge 8 --j 1 ++++

And 'header' from imod:

RO image file on unit 1 : mask.mrc Size= 432001 K

Number of columns, rows, sections ..... 480 480 480 Map mode .............................. 2 (32-bit real) Start cols, rows, sects, grid x,y,z ... 0 0 0 1 1 1 Pixel spacing (Angstroms).............. 1.000 1.000 1.000 Cell angles ........................... 90.000 90.000 90.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 0.000 0.000 Minimum density ....................... 0.0000 Maximum density ....................... 1.0000 Mean density .......................... 0.86955E-02 RMS deviation from mean................ 0.87472E-01 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 0 0 0 0

 1 Titles :

Relion 31-Jul-18 14:15:33

[Takanori Nakane]

The pixel size was not initialised correctly when you didn't apply low pass filtering. I fixed the bug. Now the header should be correct even without low pass filtering. Thank you very much for your feedback.