"Helicise: incorrect number of repeats encoutered." in segrefine3Dgrid

[Juha Huiskonen]

Hi Carsten,

I run into a problem with segrefine3Dgrid. My grid is as follows:

First parameter                          = Helical_rise_or_pitch
Second parameter                         = Helical_rotation_or_number_of_units_per_turn
Lower and upper limit first parameter    = (6.3, 6.3)
Lower and upper limit second parameter   = (16.3, 17.0)
First and second parameter increment     = (0.1, 0.1)
Rotational symmetry                      = 5

However, the run crashes wiht the following error:

    vol = vol.helicise(pixelsize, rise, -rotation, section_size)
RuntimeError: InvalidValueException at /home/eman64/EMAN2/src/eman2/libEM/sparx/emdata_sparx.cpp:6301: error with '35': 'Helicise: incorrect number of repeats encoutered.' caught

Is there something 'illegal' about this combination of helical parameters? Other parameter combinations close to these ones worked just fine earlier.

Best wishes,
Juha

[Carsten Sachse]

Hi Juha,

If you ran SEGREFINE3DGRID you should be able to find out at which grid point the actual SEGMENTREFINE3D run crashed. Could you have a look and let me know which one of the helical parameter pairs gives rise to the error?

Best wishes,

Carsten

[Juha]

Hi Carsten,

I crashes for the first one - rise 6.3 and rotation 16.3.

Best wishes,

Juha

[Carsten Sachse]

Hi Juha,

This error arises somewhat unpredictably due the helicise command I am using from the SPARX distribution. It arises from a funny combination of volume size and helical symmetry parameters. My short-term solution is to either avoid that particular combination: A small change would be sufficient, e.g. 6.31 or convert the range rather to the pitch/unit_number search space. This is my recommended way for dealing with helices. I hope this solves the problem. 

Best wishes,

Carsten

[Juha]

Hi Carsten,

Using 6.31 rise (instead of 6.3) solved the problem, many thanks.

J