Segmentmultirefine3D

[Jeremy Burgess]

% spring --version && springenv e2version.py 

GUI from package Emspring-0.83.1449

Spring environment loaded.

EMAN 2.1 alpha2 (CVS 2013/08/07 17:01:09)

Your EMAN2 is running on:  Ubuntu 12.04.4 LTS 3.2.0-60-generic x86_64

Your Python version is:  2.7.2

Hello,

I received an error during the first cycle of refinement: [during projection through reference volume]

File "/home/likewise-open/WF/01405154/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment3d/refine/sr3d_align.py", line 626, in prepare_previous_parameters_either_from_inplane_angle_or_from_previous_cycle

included_nonorientation_segments)

File "/home/likewise-open/WF/01405154/spring_v0-83-1449/lib/python2.7/site-packages/emspring-0.83.1449-py2.7.egg/spring/segment3d/refine/sr3d_align.py", line 554, in get_zero_parameters_for_initial_stages_of_refinement

psi = (-(each_result.inplane_angle + 270)) % 360

TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'

Why might the inplane_angle be a NoneType?

Thank you,

Jeremy Burgess

MSc student,

Structural Biology Research Unit,

Department of Medical Biochemistry

Centre for Imaging and Analysis,

University of Cape Town

[Carsten Sachse]

Dear Jeremy,

It is not so clear to me why this message would occur at this point. Could you please attach the parameter file in order to verify your input parameters?

Many thanks.

Best wishes,

Carsten

[Jeremy Burgess]

Hi Carsten,

The parameter file is attached:

Thank you,

Jeremy B

[Carsten Sachse]

Dear Jeremy,

I had a look at your parameter files. They do look quite similar: parameters.par is a shorter version whereas parfile_10664.par

[Carsten Sachse]

Dear Jeremy,

I had a look at your parameter files. They do look quite similar: parameters.par is a shorter version whereas parfile_10664.par is the complete version with all parameters. To make sure that really the same parameters were received by the program could you compare the header of the two report.log files and save those first lines and compare them from the two runs?

One other thing I noticed is that you used an aligned from the segmentclass run. For structure refinement stick to the one generated from 'segment' without any in-plane rotation applied. Otherwise you will have multiple unnecessary interpolation steps applied to your data. I hope this helps.

Best wishes,

Carsten