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| - I was in Houston for your last workshop on EMAn and i would like to know when we can obtain the videos from the course. | '''Q:''' I was in Houston for your last workshop on EMAn and i would like to know when we can obtain the videos from the course. |
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| (and now 18 months later, I have no idea what happened :^( ) | |
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| - I cannot get through a step of refinement. It always crashes and shows messages ERROR as followings. 'Error: ERROR - Bad statistics on this data set! 8 1e+20 nan multiply sizes different Mean=0.144097 Sigma=0.000000 Cut=0.072048 wt=4.000000 Error: ERROR - Bad statistics on this data set! 8 1e+20 nan Bad Sum Error: calcCCFX must have 2 images the same size Error, running 'classalign2 cls0037.lst finalref saverefs logit=2 keep=0.500000 mask=47 imask=-1 3 locfromfile ctfc=20.000000 quiet' on localhost'. I have checked size of images (iminfo), they look fine. All images have been phase corrected as well. What would possibly be the problem of this? Another question, does EMAN work on object with symmetry more than c10? |
'''Q:''' I am trying to refine a structure with D7 symmetry using Eman1.8. It seemed the sym=d7 did not work at all (even one rough refinement with sym=d7 command resulted in a wrong structure). Is it a bug? Do you have any suggestion? Thank you. |
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| This message usually means your threed.0a.mrc and your start.hed file don't have the same dimensions (in pixels). Yes, EMAN can handle arbitrary high C symmetries, assuming your sampling is fine enough to resolve the individual asymmetric units... |
'''A:''' Please provide the exact 'refine' command you used (which did not work). startAny doesn't really do symmetry, and startcsym (which is what you should use) does only C7 symmetry. The idea would be to use startcsym with C7 symmetry then use proc3d to impose D7 symmetry on the final result. I think all of this is discussed in the tutorial interface if you tell it you're doing a D7 reconstruction. ---Thank you. My refine command that is not working on d7 symmetry: refine 6 ang=15.0 sym=d7 mask=60 pad=128 hard=25 classkeep=1 classiter=8 xfiles=2.54,900,99 phasecls shrink=4 proc=6 median. I am pretty confident that the particles are good (2D averages show clearly d7 symmetry of the particles). I managed to generate starting model with d7 symmetry using eman2 command (e2make3d.py 2d.img --sym=d7 --out=0d.mrc --pad=128). The starting model generated is good. However, after only one iteration of refinement, the structure has already changed a lot (only center part of the particle is remained). |
Q: I was in Houston for your last workshop on EMAn and i would like to know when we can obtain the videos from the course.
They are being converted, but it is a slow process. They should be available on the workshop page when done.
(and now 18 months later, I have no idea what happened :^( )
Q: I am trying to refine a structure with D7 symmetry using Eman1.8. It seemed the sym=d7 did not work at all (even one rough refinement with sym=d7 command resulted in a wrong structure). Is it a bug? Do you have any suggestion? Thank you.
A: Please provide the exact 'refine' command you used (which did not work). startAny doesn't really do symmetry, and startcsym (which is what you should use) does only C7 symmetry. The idea would be to use startcsym with C7 symmetry then use proc3d to impose D7 symmetry on the final result. I think all of this is discussed in the tutorial interface if you tell it you're doing a D7 reconstruction.
---Thank you. My refine command that is not working on d7 symmetry: refine 6 ang=15.0 sym=d7 mask=60 pad=128 hard=25 classkeep=1 classiter=8 xfiles=2.54,900,99 phasecls shrink=4 proc=6 median. I am pretty confident that the particles are good (2D averages show clearly d7 symmetry of the particles). I managed to generate starting model with d7 symmetry using eman2 command (e2make3d.py 2d.img --sym=d7 --out=0d.mrc --pad=128). The starting model generated is good. However, after only one iteration of refinement, the structure has already changed a lot (only center part of the particle is remained).