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pipeline:meridien:sp_higher_ord_abber [2021/03/16 10:52]
aali 		pipeline:meridien:sp_higher_ord_abber [2021/03/22 16:40]
aali
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 : The SPHIRE module provides a wrapper around the ctf refinement command. : The SPHIRE module provides a wrapper around the ctf refinement command.
  
-: After running the ctf refinement routine, the wrapper automatically converts the star file and apply beam tilt correction on the star2BDB converted stack so that it can be used directly for further processing. (still in test phase). +: After running the ctf refinement routine, the wrapper automatically converts the star file and apply beam tilt correction on the star2BDB converted stack so that it can be used directly for further processing. (still in test phase).
  
 </code> </code>
  
 ===== Input ===== ===== Input =====
 +
 === Main Parameters === === Main Parameters ===
  
-  ; post_refine_folder : The user has to be provide the location of the post refiner directory so that the script can automatically detect all the required information for the polishing. (default required string) +  ; post_refine_folder : : Input folder is the directory where the results of the post refiner are present and python routine automatically locates all the required files used for ctf refinement. (default required string)  
-  ; motioncorr_starfile : The metadata star file which is being generated by MotionCorr. (default required string) +  ; output_folder : : Output folder is the directory where all the results of the ctf refinement are saved. (default required string)  
-  ; output_directory : Toplevel directory where outputs will be written. (default required string) +  ; <nowiki>--</nowiki>estimate_magnification : : Estimate magnification of dataset . (default False)  
-  ; %%--%%training_params : In case if the user wants to do the training part of the polishing then this is None. Otherwise provide the optimize_params.txt file. (default none) +  ; <nowiki>--</nowiki>estimate_beamtilt : : Estimate beamtilt from the dataset. (default False)  
-  ; %%--%%min_no_particles : Number of particles to inlcude for training. (default 5000) +  ; <nowiki>--</nowiki>estimate_trefoil : : estimate 3-fold astigmatism per optics group .(default False)  
-  ; %%--%%submission_template :  Submission template for MPI command. In case of running this tool on a cluster, always a submission template. The number of MPI processors and threads in the submission template should be the same as the one specified below in the MPI procs and threads value.(default none) +  ; <nowiki>--</nowiki>estimate_order_aberation : : Estimate the 4th order aberation .(default False)  
-  ; %%--%%submission_command : Submission commmand for cluster (default sbatch) +  ; <nowiki>--</nowiki>perform_CTF_params_fit : : Perform CTF parameter fitting. (default False)  
-  ; %%--%%relion_mpirun_executable :  Since there can be more than one mpirun environment installed on a workstation or on a cluster. It can be sometimes necessary to provide the relion specific mpirun executable. Just type which mpirun -a in a terminal and choose the one which relion requires. (default mpirun) +  ; <nowiki>--</nowiki>fit_defocus_micrograph : : Fit defocus based on micrographs. (default False)  
-  ; %%--%%relion_polishing_executable : Similar to the issue of relion mpirun executable, it can be sometime necessary to provide the specific relion polishing executable also. Just type which relion_motion_refine_mpi and copy the path here. (default relion_motion_refine_mpi) +  ; <nowiki>--</nowiki>fit_defocus_particle : : Fit defocus based on particles. (default False)  
-  ; %%--%%mpi_procs :  The number of MPI processors used for Relion multiprocessing. For training part only one MPI processors is used. In case when running the program on cluster, the MPI processors value should be same as used in the submission template.(default 1) +  ; <nowiki>--</nowiki>fit_astigmatism_micrograph : : Fit astigmatism based on micrographs .(default False)  
-  ; %%--%%no_of_threads :  The number of threads use during the polishing. In case when running the program on cluster, the thread value should be same as used in the submission template.(default 1)+  ; <nowiki>--</nowiki>fit_astigmatism_particle : : Fit astigmatism based on particles. (default False)  
 +  ; <nowiki>--</nowiki>fit_bfactor_micrograph : : Fit bfactor based on micrographs. (default False)  
 +  ; <nowiki>--</nowiki>fit_bfactor_particle : : Fit bfactor based on particles. (default False)  
 +  ; <nowiki>--</nowiki>fit_phase_shift_micrograph : : Fit phase shift estimation for micrographs .(default False)  
 +  ; <nowiki>--</nowiki>fit_phase_shift_particle : : Fit phase shift estimation for particles. (default False)  
 +  ; <nowiki>--</nowiki>min_res_fit : : minimum resolution value for fitting (default 30.0)  
 +  ; <nowiki>--</nowiki>submission_template : : Submission template for MPI command. In case of running this tool on a cluster, always a submission template. The number of MPI processors and threads in the submission template should be the same as the one specified below in the MPI procs and threads value.(default none) ; ; <nowiki>--</nowiki>submission_command : : Submission commmand for cluster (default sbatch) ; ; <nowiki>--</nowiki>relion_mpirun_executable : : Since there can be more than one mpirun environment installed on a workstation or on a cluster. It can be sometimes necessary to provide the relion specific mpirun executable. Just type which mpirun -a in a terminal and choose the one which relion requires. (default mpirun) ; ; <nowiki>--</nowiki>relion_ctfrefine_executable : : Similar to the issue of relion mpirun executable, it can be sometime necessary to provide the specific relion polishing executable also. Just type which relion_ctf_refine_mpi and copy the path here. (default relion_ctf_refine_mpi) ; ; <nowiki>--</nowiki>mpi_procs : : The number of MPI processors used for Relion multiprocessing. For training part only one MPI processors is used. In case when running the program on cluster, the MPI processors value should be same as used in the submission template.(default 1) ; ; <nowiki>--</nowiki>no_of_threads : : The number of threads use during the polishing. In case when running the program on cluster, the thread value should be same as used in the submission template.(default 1)
  
-\\ 
 === Advanced Parameters === === Advanced Parameters ===
  
-  ; %%--%%first_frame : The 1st frame number from where it should start. (default 1) +; ; <nowiki>--</nowiki>mrc_reloc_folder : : In case if the mrcs images were moved from original location where they were generated to a new location. Then the user has to provide a path directory link to the new location . (default none)
-  ; %%--%%last_frame : The last frame number where it should end. (default -1) +
-  ; %%--%%bfac_minfreq :  The minimum frequency range which is normally the maximum inner shell to include in enhancement. (default 20) +
-  ; %%--%%bfac_maxfreq :  The minimum frequency range which is normally the maximum outer shell to include in enhancement. (default -1) +
-  ; %%--%%mrc_reloc_folder : In case if the mrcs images were moved from original location where they were generated to a new location. Then the user has to provide a path directory link to the new location . (default none)+
  
 ===== Output ===== ===== Output =====
-  ; shiny.star : Output star file for polishing particles. + 
-  ; bdb:polished_stack : : Polished particles stack. +; ; particles_ctf_refine.star : : Output star file for ctf refined stack. 
-  ; BDB2STAR : Using sphire2relion tool , the bdb stack is converted to star file so that it can be used in relion. The star file is saved in BDB2STAR folder. +; ; bdb:ctfrefine_stack : :  Ctf refined particles stack. (still in test phase) 
-  ; PostProcess : Since the input to the tool is Post refiner directory, the tool can automatically create the necessary file in PostProcess folder which is necessary to provide for polishing.+; ; BDB2STAR : : Using sphire2relion tool , the bdb stack is converted to star file so that it can be used in relion. The star file is saved in BDB2STAR folder.  
 +; ; PostProcess : : Since the input to the tool is Post refiner directory, the tool can automatically create the necessary file in PostProcess folder which is necessary to provide for ctf refinement.
  
 =====   ===== =====   =====
Line 64: Line 67:
  
 <code> <code>
-module unload sphire (unload the module sphire) +module unload sphire (unload the module sphire)
  
-module load sphire/clem/Polishing_SPHIRE_v1.2 or sphire/clr/Polishing_SPHIRE_v1.2 (this has to be done only in case if you have a different installation then the default one, since this tool is still not released, the git branch is different). +module load sphire/clem/Polishing_SPHIRE_v1.2 or sphire/clr/Polishing_SPHIRE_v1.2 (this has to be done only in case if you have a different installation then the default one, since this tool is still not released, the git branch is different).
  
 module load relion module load relion
pipeline/meridien/sp_higher_ord_abber.txt · Last modified: 2021/03/22 16:49 by aali

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