Changes between Initial Version and Version 1 of Ticket #7722, comment 5


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Timestamp:
Oct 4, 2022, 11:55:48 AM (3 years ago)
Author:
Tom Goddard

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  • Ticket #7722, comment 5

    initial v1  
    33The traceback is an entirely different problem and a bug in Segger.  You might try opening the session in ChimeraX 1.4 or better a ChimeraX daily build.  You reported the bug for ChimeraX 1.3 and I've made various Segger fixes since then.  But I don't think I fixed this one.  Segger was developed by Greg Pintilie for Chimera.  I ported it to ChimeraX but Greg is still using old Chimera and Segger is 30000 lines of code so I have not been able to fix a lot of the problems.  Been hoping the Greg will start using ChimeraX.
    44
    5 At any rate, looking at the Segger code it appears to me that the transform that is None that is causing this problem is because the volume data associated with the segmentation is not being loaded, maybe because the original volume file was found.  The transform that causes the error comes from that volume file and is None when the volume is not available.  The code should handle this better so it does not try to use the transform when the volume is not loaded.  If you make sure the original volume file is still available where the Segger session file expects to find it then it will probably work without this error.
     5At any rate, looking at the Segger code it appears to me that the transform that is None that is causing this problem is because the volume data associated with the segmentation is not being loaded, maybe because the original volume file was not found.  The transform that causes the error comes from that volume file and is None when the volume is not available.  The code should handle this better so it does not try to use the transform when the volume is not loaded.  If you make sure the original volume file is still available where the Segger session file expects to find it then it will probably work without this error.
    66
    77I see I put a fix in for this problem 7 months ago, so it is in ChimeraX 1.4.  But the fix was to make Segger add the needed transform to the session file when it is saved so if it gets restored without the volume it still knows the transform.  By the way, the transform goes from the volume i,j,k grid indices to their x,y,z positions (in Angstroms) so usually just encodes the volume grid spacing.  So if you saved your Segger session in ChimeraX 1.3, this fix does not help because the session file simply does not have the information if restoring it cannot find the original volume file.