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Venkata Prasad Dandey
May 27, 2014, 7:28:17 AM5/27/14
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Dear Carsten,
I have recently updated to new version of Spring. I am now using the latest version Emspring(0.82.1339dev).
Thanks for including "Gold standard refinement" in the new version. When I run the "segmentrefine3d" from the scratch it works well, but when I am trying to do the refinement with option "Continue refinement", I get below error and the parameters used. how to solve this issue?
regards,
venkat
INFO:CPU0:evaluate_alignment_parameters_and_summarize_in_plot:Image processing statistics summary:
----------------------------------------------------------- ----------- ---------
Resolution at FSC (0.5/0.143) (Angstrom) 28.5867 21.44
Number of asymmetric units (before/after symmetrization) 2448 7344
Helical rise/rotation (Angstrom/degrees) 14.2 53
Total length of helices including/excluding ends (Angstrom) 918339 428339
Number of included/total segments 2448 15785
Number of micrographs/helices 72 490
Alignment size/segment step size (Angstrom) 500 14
Pixel size on the specimen (Angstrom) 1.34
----------------------------------------------------------- ----------- ---------
Traceback (most recent call last):
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/bin/segmentrefine3d_mpi", line 125, in <module>
sys.exit(spring.segment3d.refine.sr3d_mpi.main())
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/segment3d/refine/sr3d_mpi.py", line 1153, in main
segment_stack.perform_iterative_projection_matching_and_3d_reconstruction()
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/segment3d/refine/sr3d_mpi.py", line 1125, in perform_iterative_projection_matching_and_3d_reconstruction
pixelinfo, ref_cycle_id)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/segment3d/refine/sr3d_main.py", line 868, in compute_cross_fsc_and_write_out_merged_volume
self.update_highest_fsc_database(ref_cycle_id, model_fscs, model_resolution)
File "/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/lib/python2.7/site-packages/emspring-0.82.1339dev-py2.7.egg/spring/segment3d/refine/sr3d_main.py", line 811, in update_highest_fsc_database
model_0143, model_05 = zip(*model_resolution)
ValueError: need more than 0 values to unpack
Rank 0 on machine cina-dw01.ethz.ch with process ID 24875 raised an error message. Find the corresponding error message above. All other MPI processes are aborted. Ignore the error messages thereafter as they can arise as a result of the aborting procedure.
INFO:vdandey:/net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/parts/openmpi/bin/mpirun -np 32 /net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/bin/springenv /net/bs-sw/sw-repo/cina/csachse-emspring-454a5fe5b8d1/bin/python cleanup.py
logged on Mon, 26 May 2014 16:56:44
----------------------------------------------------------------------------------------------------
The final set of parameters has been completed with the provided default parameters:
INFO:CPU0:startlog:Image input stack refinement = /mnt/Cache-SSD/PYD_14012014/segment_29_Mar_2014_19_56_24_43468/PYD_20estack.hdf
INFO:CPU0:startlog:Output volume name = recvol.hdf
INFO:CPU0:startlog:Diagnostic plot prefix = diagnostic_plot.pdf
INFO:CPU0:startlog:Number of iterations = 20
INFO:CPU0:startlog:Reference structure option = False
INFO:CPU0:startlog:Reference volume = reference_vol.hdf
INFO:CPU0:startlog:spring.db file = /mnt/Cache-SSD/PYD_14012014/segmentrefine3d_22_May_2014_14_59_16_45046/spring.db
INFO:CPU0:startlog:Continue refinement option = True
INFO:CPU0:startlog:refinement.db file = /mnt/Cache-SSD/PYD_14012014/segmentrefine3d_22_May_2014_14_59_16_45046/refinement020.db
INFO:CPU0:startlog:Assemble refinement strategy = True
INFO:CPU0:startlog:LR - Low resolution aim = False
INFO:CPU0:startlog:LR - azimuthal and out-of-plane search restraint in degrees = (180.0, 180.0)
INFO:CPU0:startlog:LR - X and Y translation range in Angstrom = (50, 23)
INFO:CPU0:startlog:MR - Medium resolution aim = False
INFO:CPU0:startlog:MR - azimuthal and out-of-plane search restraint in degrees = (180.0, 180.0)
INFO:CPU0:startlog:MR - X and Y translation range in Angstrom = (21, 10)
INFO:CPU0:startlog:HR - High resolution aim = False
INFO:CPU0:startlog:HR - azimuthal and out-of-plane search restraint in degrees = (180.0, 180.0)
INFO:CPU0:startlog:HR - X and Y translation range in Angstrom = (50, 23)
INFO:CPU0:startlog:MaxR - Maximum resolution aim = True
INFO:CPU0:startlog:MaxR - azimuthal and out-of-plane search restraint in degrees = (4.0, 4.0)
INFO:CPU0:startlog:MaxR - X and Y translation range in Angstrom = (7, 14)
INFO:CPU0:startlog:Absolute X and Y translation limit in Angstrom = (100, 100)
INFO:CPU0:startlog:Independent half-set refinement = True
INFO:CPU0:startlog:Half-set refinement start = max
INFO:CPU0:startlog:High-pass filter option = False
INFO:CPU0:startlog:Low-pass filter option = True
INFO:CPU0:startlog:High and low-pass filter cutoffs in 1/Angstrom = (0.001, 0.09)
INFO:CPU0:startlog:B-Factor = 0
INFO:CPU0:startlog:Custom filter option = False
INFO:CPU0:startlog:Custom-built filter file = filter_function.dat
INFO:CPU0:startlog:Automatic FSC filter = True
INFO:CPU0:startlog:Filter layer-lines option = False
INFO:CPU0:startlog:Micrographs select option = False
INFO:CPU0:startlog:Include or exclude micrographs = include
INFO:CPU0:startlog:Micrographs list = 1-9, 11, 13
INFO:CPU0:startlog:Helices select option = False
INFO:CPU0:startlog:Include or exclude helices = include
INFO:CPU0:startlog:Helices list = 1-9, 11, 13
INFO:CPU0:startlog:Segments select option = False
INFO:CPU0:startlog:Include or exclude segments = include
INFO:CPU0:startlog:Segment file = stackid_file.dat
INFO:CPU0:startlog:Classes select option = False
INFO:CPU0:startlog:Include or exclude classes = include
INFO:CPU0:startlog:Class type = class_id
INFO:CPU0:startlog:Classes list = 1-9, 11, 13
INFO:CPU0:startlog:Persistence class option = False
INFO:CPU0:startlog:Persistence class length in Angstrom = 700
INFO:CPU0:startlog:Class occupancy threshold = 0.5
INFO:CPU0:startlog:Straightness select option = False
INFO:CPU0:startlog:Include or exclude curved helices = include
INFO:CPU0:startlog:Curvature range = (0.0, 1e-05)
INFO:CPU0:startlog:Layer line correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on layer-line correlation = include
INFO:CPU0:startlog:Correlation layer line range = (0.6, 1.0)
INFO:CPU0:startlog:Defocus select option = True
INFO:CPU0:startlog:Include or exclude defocus range = include
INFO:CPU0:startlog:Defocus range = (10000, 30000)
INFO:CPU0:startlog:Astigmatism select option = False
INFO:CPU0:startlog:Include or exclude astigmatic segments = include
INFO:CPU0:startlog:Astigmatism range = (0, 4000)
INFO:CPU0:startlog:Projection correlation select option = False
INFO:CPU0:startlog:Include or exclude segments based on projection correlation = include
INFO:CPU0:startlog:Correlation projection range = (1.0, 1.0)
INFO:CPU0:startlog:Out-of-plane tilt select option = False
INFO:CPU0:startlog:Include or exclude out-of-plane tilted segments = include
INFO:CPU0:startlog:Out-of-plane tilt range = (-5, 5)
INFO:CPU0:startlog:Shift normal to helix select option = False
INFO:CPU0:startlog:Include or exclude segments with shift normal to helix = include
INFO:CPU0:startlog:Shift normal to helix in Angstrom = 5.0
INFO:CPU0:startlog:Keep intermediate files = False
INFO:CPU0:startlog:Estimated helix inner and outer diameter in Angstrom = (10, 100)
INFO:CPU0:startlog:Pixel size in Angstrom = 1.34
INFO:CPU0:startlog:Symmetrize helix = True
INFO:CPU0:startlog:Helical rise/rotation or pitch/number of units per turn choice = rise/rotation
INFO:CPU0:startlog:Enforce even phi option = False
INFO:CPU0:startlog:Release cycle even phi = 8
INFO:CPU0:startlog:Pitch enforce even phi = 8.0
INFO:CPU0:startlog:Bin cutoff of phi angles = 100
INFO:CPU0:startlog:Helical symmetry in Angstrom or degrees = (14.2, 53.0)
INFO:CPU0:startlog:Rotational symmetry = 3
INFO:CPU0:startlog:Helix polarity = polar
INFO:CPU0:startlog:Unbending option = False
INFO:CPU0:startlog:Force helical continuity = True
INFO:CPU0:startlog:Limit in-plane rotation = True
INFO:CPU0:startlog:Delta in-plane rotation angle = 10.0
INFO:CPU0:startlog:Out-of-plane tilt angle range = (-14, 14)
INFO:CPU0:startlog:Number of projections azimuthal/out-of-plane angle = (240, 7)
INFO:CPU0:startlog:Image alignment size in Angstrom = 330
INFO:CPU0:startlog:Step size of segmentation in Angstrom = 14
INFO:CPU0:startlog:3D CTF correction = True
INFO:CPU0:startlog:3D CTF correction intensity = low
INFO:CPU0:startlog:MPI option = True
INFO:CPU0:startlog:Number of CPUs = 48
INFO:CPU0:startlog:Temporary directory = /local0/tmp
INFO:CPU0:startlog:
Carsten Sachse
May 28, 2014, 3:27:07 AM5/28/14
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Hi Venkat,
Thanks for pointing this out. Could you also send me the parameter file of the run before the 'continue refinement' run?
Thanks.
Best wishes,
Carsten
Venkata Prasad Dandey
May 28, 2014, 5:37:48 AM5/28/14
to emsp...@googlegroups.com
Dear Carsten,
I have attached the parameter file of the previous run. If you look into this file, I first tried with "continue refinement" by updating the data base of the previous run ( because it was run with old version) and the error is same. So, I tried without continue refinement option.
regards,
venkat
I have attached the parameter file of the previous run. If you look into this file, I first tried with "continue refinement" by updating the data base of the previous run ( because it was run with old version) and the error is same. So, I tried without continue refinement option.
regards,
venkat
Carsten Sachse
Jun 7, 2014, 3:35:09 PM6/7/14
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Dear Venkat,
I tried to re-create the error you obtained and I have not been successful. The SPRING refinement strategies work like you instructed them including the 'continue refinement option' with a test data set from TMV.
I believe that your data somehow has very few segments left after selection. Is it possible that your data set is too small for an independent half-set refinement?
Best wishes,
Carsten
On Tuesday, May 27, 2014 1:28:17 PM UTC+2, Venkata Prasad Dandey wrote:
On Tuesday, May 27, 2014 1:28:17 PM UTC+2, Venkata Prasad Dandey wrote:
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