tlt axis

[Reza Khayat]

Hi,

I have a tilt series whose tilt axis varies considerably during the tomogram refinement -see tilt parameters below. 

"tlt_params": [[173.26799026841906,288.7358941343882,475.56390919624073,-40.790276713425854,-45.5274403834123],
[183.0488252557279,324.8802711177549,474.5502286410027,-38.02122781802894,-47.41314899509714],
[168.81510754251684,248.54884380794138,473.74191156527996,-34.62043994178885,-48.118751125832],
[138.83414742079435,270.2558131516294,472.9132832716252,-31.63179929797964,-49.832450814029826],
[143.0434253065862,315.86994943851096,112.23530356939739,-29.073049137383492,-51.12609939991002],
[134.55755707249585,272.3699506487204,112.44968272718882,-27.284637964135293,-52.060345583751875],
[137.9641671906896,284.7701034095117,111.9591918240218,-23.738055761904302,-52.36500875061471],
[177.4269872756717,307.9720353821988,111.70412884268612,-20.573011314094476,-54.071001937504604],
[143.95314585556943,255.3283529663546,111.33309157019907,-17.92773062463634,-54.48097163322909],
[160.72163292294508,341.8471906080086,111.35307023238897,-14.990961385956114,-55.7661505102744],
[151.87165800115713,319.7731634714952,111.73112095493859,-11.47852271858083,-57.04985804133955],
[182.65462906856638,315.5903133947691,111.47676305492841,-8.829700694453837,-56.04442879944745],
[125.4060647597715,349.39952704913935,111.61220341743727,-5.506342020737015,-56.861672167585986],
[164.0827261968798,233.02073496051318,111.14455525104245,-3.185812682647855,-56.03917956674752],
[94.29177509282857,179.17216378345705,111.49077267855688,-0.557092469134118,-57.14301052153005],
[137.2945868571567,118.25957922222331,111.38051521792364,2.2612702993202927,-58.07619103137729],
[144.52558792464703,124.31983328950395,111.38801232958569,5.624863526095156,-59.06047565680616],
[20.661946376024467,-9.580617889521017,110.81202179051299,9.113388368191373,-60.2858789423044],
[141.69882538021616,161.98832383839397,111.3152638692206,11.39827747033874,-60.958964730296834],
[152.8031376004145,97.65528085282786,111.52989985905165,14.298922291380347,-61.31907263558014],
[150.74833056215067,153.1305861026905,111.61410246368656,17.411548102241447,-61.41266198717705],
[138.19887606655834,48.13762490987225,112.06105893307824,20.544673108981335,-62.391580197813916],
[145.17844438697568,156.49082442439527,111.70326651578833,22.55775278123655,-62.0783832642973],
[181.96034223617065,6.8813377400961375,111.93332696314482,25.946401328627623,-62.402773283670065],
[139.7258439147701,113.34367838695539,112.11890640773039,28.280592130147706,-63.62908511807397],
[159.78206311304515,12.964351478385689,113.42513263702295,31.74172029748902,-66.97845393554263],
[142.40683628452226,137.92981956370346,114.01876635597462,34.45614530297294,-66.82606893877282],
[138.52364238408305,17.862841060615185,114.60243331263692,37.86313611371853,-67.85010183400861],
[129.45238688557924,22.95911874571606,115.21996401729386,40.964851623595365,-69.31982282338039],
[138.73435895431464,-13.670557514553519,116.2038782713118,43.27058776793701,-70.41225665565958],
[126.8387440123674,-24.71084385971286,116.41906011179297,45.83323772808901,-71.34146982235242],
[136.4951390921894,2.434593273935059,118.34254124399232,48.544200675146556,-72.69607215299087],
[82.57119833398517,-31.801752288085027,120.18147968157155,51.52464014965537,-74.45029335993478],
[89.39861473415365,-34.95254370973501,121.81177491347431,55.51743402780873,-77.18339275966522]

Other tilt series from the same data collection refine without any issues. The tlt axis values for the other tilt series is -95deg. There are no significant jumps in the problematic tilt-series. In fact, EMAN2.99.66 aligns the problematic tilt series fine (the ali_XX.hdf in the tomorecon_XX) directories. However, the tomogram is another story since the tilt axis is out of wack. Any suggestions on how to fix this problem? I don't want to discard the tilt series as it's one of the most informative tilt series I have. 

Best wishes,
Reza

[Muyuan Chen]

What is the e2tomogram command? It may be an issue in patch tracking where it tries to place the sample at the x-y plane. It is a bit odd to have such a large impact though. 

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[Reza Khayat]

/home/rkhayat/Applications/miniforge3/envs/eman2/bin/e2tomogram.py tiltseries/2024Aug05_53kx_ts_38_Align.hdf --autoclipxy --zeroid=-1 --rawtlt=tiltseries/2024Aug05_53kx_ts_38_Align.tlt --tltax=-94.5 --npk=20 --tltkeep=1 --niter=2,1,1,1 --maxshift=0.2 --outsize=1k --bytile --pkkeep=0.9 --compressbits=5 --clipz=640 --bxsz=64 --correctrot --rmbeadthr=-1.0 --threads=20 --patchtrack=0 --tltrange=-60,60 --pk_maxval=1.1

[Muyuan Chen]

I don't recall making any changes to the landmark based refinement (niter=xxxx) recently. The only related change I made was the exclusion of bad tilt images. Did it report many bad tilt images in the process? Does it work if you remove --correctrot option? If none works, maybe you can pass me the tilt series file and I can check. 

To view this discussion visit https://groups.google.com/d/msgid/eman2/3cce5f52-063b-405b-abe7-8bd6da678327n%40googlegroups.com.

[Reza Khayat]

Wow, removing the --correctrot flag fixed the problem! Thanks.

Best wishes,