Closed sjweaver closed 6 years ago
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?
Thank you very much for reporting this. This is unintentional. The option will be back in RELION 3.0.
Ok, thanks! That clarifies things :)
Any sneak peek on when approx RELION 3.0 is coming???
The following tweet from Sjors is the latest news :-) https://twitter.com/SjorsScheres/status/994855712185569281
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
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