--nr_uniform flag in relion_project is broken?

[sjweaver]

Hi all,

Thanks for your work on Relion! I'm trying to use relion_project to generate 2D projections of a 3D map, but it no longer seems to recognize the --nr_uniform flag. The same issue was reported on the list in March (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCPEM;42c4516a.1803). I'm running Relion2.1.0 on sbgrid.

20180425_creatingprojections]$ relion_project +++ RELION: command line arguments (with defaults for optional ones between parantheses) +++ ====== Options ===== --i : Input map to be projected --o (proj) : Rootname for output projections --ctf (false) : Apply CTF to reference projections --ctf_phase_flip (false) : Flip phases of the CTF in the output projections --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? --angpix (1) : Pixel size (in Angstroms) --mask () : Mask that will be applied to the input map prior to making projections --ang (None) : STAR file with orientations for multiple projections (if None, assume single projection) --rot (0) : First Euler angle (for a single projection) --tilt (0) : Second Euler angle (for a single projection) --psi (0) : Third Euler angle (for a single projection) --xoff (0) : Origin X-offsets (in pixels) (for a single projection) --yoff (0) : Origin Y-offsets (in pixels) (for a single projection) --zoff (0) : Origin Z-offsets (in pixels) (for a single 3D rotation) --add_noise (false) : Add noise to the output projections (only with --ang) --white_noise (0) : Standard deviation of added white Gaussian noise --model_noise () : Model STAR file with power spectra for coloured Gaussian noise --subtract_exp (false) : Subtract projections from experimental images (in --ang) --ignore_particle_name (false) : Ignore the rlnParticleName column (in --ang) --3d_rot (false) : Perform 3D rotations instead of projection into 2D images --maxres (-1) : Maximum resolution (in Angstrom) to consider in Fourier space (default Nyquist) --pad (2) : Padding factor --ctf2 (false) : Apply CTF*CTF to reference projections --NN (false) : Use nearest-neighbour instead of linear interpolation

20180425_creatingprojections]$ relion_project --i j344_postprocess_masked_D2.mrc --o j344_proj --angpix 0.8315 --nr_uniform 50 The following warnings were encountered upon command-line parsing: WARNING: Option --nr_uniform is not a valid RELION argument Reading map: j344_postprocess_masked_D2.mrc Done reading map! Done writing j344_proj

It looks like the projection images file has 8428099 z slices??

20180425_creatingprojections]$ header j344_proj

RO image file on unit 1 : j344_proj Size= 371 K

                This is a byte-swapped file.

                This file has an old-style MRC header.

     This file has invalid axis indices, adjusting them to 1,2,3

Number of columns, rows, sections ..... 32831 39491 8428099 Map mode .............................. 0 (byte)
Start cols, rows, sects, grid x,y,z ...32831 0 0 1 1 1 Pixel spacing (Angstroms).............. 1.000 1.000 1.000
Cell angles ........................... 0.000 0.000 0.000 Fast, medium, slow axes ............... X Y Z Origin on x,y,z ....................... 0.000 0.000 0.000
Minimum density ....................... 0.0000
Maximum density ....................... 0.0000
Mean density .......................... 0.55340E-40 tilt angles (original,current) ........ 0.0 0.0 0.0 0.0 0.0 0.0 Space group,# extra bytes,idtype,lens . 39492 0 0 0

 0 Titles :

[daryna-smyrnova]

Same problem for me. Relion 2.1.0

As I can see from the code in project.cpp - the option is no longer there. Shall we use --ang option with angle distribution *star file instead?

Maybe something should be changed in the tutorial as well?

[biochem-fan]

Thank you very much for reporting this. This is unintentional. The option will be back in RELION 3.0.

[daryna-smyrnova]

Ok, thanks! That clarifies things :)

Any sneak peek on when approx RELION 3.0 is coming???

[biochem-fan]

The following tweet from Sjors is the latest news :-) https://twitter.com/SjorsScheres/status/994855712185569281