[3dem] anisotropic magnification distortion correction with mag_distortion_estimate/correct

Fri Aug 14 13:30:48 PDT 2020

Hello, Marin,

Thank you for your quick response. I read your paper, and now I understand why we shouldn't use the anisotropic magnification estimation from a separated measurement. I will look into the water rings in my dataset. Please excuse me for not having much experience with IMAGIC-4D, would you please explain more specifically on how the anisotropic magnification distortion is measured from the water rings and corrected in IMAGIC-4D?

Best,
Yuejiao Xian

________________________________
From: Marin van Heel <marin.vanheel at googlemail.com>
Sent: Friday, August 14, 2020 11:34 AM
To: Xian, Yuejiao <yxian at miners.utep.edu>
Cc: 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>; Yuejiao Xian <xianyuejiao at gmail.com>
Subject: Re: [3dem] anisotropic magnification distortion correction with mag_distortion_estimate/correct

Dear Yuejiao Xian

I had a quick look at your data and I noticed that you have significant power anisotropy in your gold grating images.
It is a better idea in general to use the dataset itself rather than to get the anisotropy from a separate measurement!
Use the water-rings in the main eigenvectors of the amplitude spectra as per our paper.
(
Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin
<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAfanasyev*2C*2520P.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=B*2FOZQY12839MrPCFaMs7iQFYFZp9ISeIqKl4FbXUbZI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll9mOFmqpA$ >
P. Afanasyev<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAfanasyev*2C*2520P.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=B*2FOZQY12839MrPCFaMs7iQFYFZp9ISeIqKl4FbXUbZI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll9mOFmqpA$ >, C. Seer-Linnemayr<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DSeer-Linnemayr*2C*2520C.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=rXnLF76nGQg7Bp2AJkLAf2FpMdT9VsPjQWt7fZhLh3I*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll9687XyCA$ >, R. B. G. Ravelli<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DRavelli*2C*2520R.B.G.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=TiP8EhhDCOfHRD2JqA7wah*2BpsZrxhGybnBtvcIG1xGA*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll_TIoseqw$ >, R. Matadeen<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DMatadeen*2C*2520R.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=*2B5n*2FImpIH3VyQL*2F61vl1AHql5SOTFBgxi5nd3jtQPWY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll-7FBcbxQ$ >, S. De Carlo<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DDe*2520Carlo*2C*2520S.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=tMsvnrA0DUqjopvUrQANxaLQbf41Tvy*2F8fxIsP7pVU8*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll_vSlc84g$ >, B. Alewijnse<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DAlewijnse*2C*2520B.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=HXJ865N*2FqkVjSYsR0qtW4nhrZHLWuMXcuqRwoenUzUY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll-bwUG_ng$ >, R. V. Portugal<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DPortugal*2C*2520R.V.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=siaDFlLRuBHt9R*2FSjlNQ5vQdtMclAAHgtf6k5ZJpjOI*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll9ZO8qMrw$ >, N. S. Pannu<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DPannu*2C*2520N.S.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=vF96R8xSbP64iln7Bq8i*2FznYmLiphhkXqzHu80vxsLM*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll_Yv2DfNA$ >, M. Schatz<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3DSchatz*2C*2520M.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=hXF5*2B*2BrPyBLvYyD2Fbxo5yyZWFRQ8Bx1dTjyFQE0PXk*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSU!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll-xlt8XkQ$ > and M. van Heel<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fscripts.iucr.org*2Fcgi-bin*2Fcitedin*3Fsearch_on*3Dname*26author_name*3Dvan*2520Heel*2C*2520M.&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=WzrD9tHHWU6f18N2qNLfTUeUa1DYEg5wYWR8T9f4iVc*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll87tntpaQ$ >
)

Cheers,
Marin

https://urldefense.com/v3/__https://journals.iucr.org/m/issues/2017/05/00/kf5002/index.html__;!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll82lw40qg$ <https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fjournals.iucr.org*2Fm*2Fissues*2F2017*2F05*2F00*2Fkf5002*2Findex.html&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=Up1qs4p8vHdnq*2FBYmAxII67iNiSP4QLxzWfnAMJBCPE*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUl!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll9OsgiSLg$ >

[image.png]

On Fri, Aug 14, 2020 at 2:50 PM Xian, Yuejiao <yxian at miners.utep.edu<mailto:yxian at miners.utep.edu>> wrote:

Hello, all.

I am trying to estimate the anisotropic magnification distortion from a cryo-EM dataset, however, I am not sure if I got the accurate estimation. I appreciate any comments or suggestions.  Here is what I did:

I stacked about 70 gold grating images into one mrc file, which I used as the input of the mag_distortion_estimate program developed by Timothy Grant and Nikolaus Grigorieff. Here is the output parameter:

=====================================

The following distortion parameters were found :-

Distortion Angle     = 112.6

Major Scale          = 1.001

Minor Scale          = 0.999

 Stretch only parameters would be as follows :-

Distortion Angle     = 112.6

Major Scale          = 1.002

Minor Scale          = 1.000

Corrected Pixel Size = 0.669

The Total Distortion = .15%

=========================================

 The outputted ring images are attached. The ring on the left is the combined ring before any distortion correction, the one in the middle is the rotational averaged ring, the one in the right is the ring after distortion correction.

To verify if the parameters are accurate,  I then took the three parameters ( highlighted in bold) and the same stack file as an input for mag_distortion_correct to correct the distortion. With the corrected stack file, I then estimated the distortion again, and it showed the images still have 0.15% distortion, with the following parameters:

=========================================

Distortion Angle     = 21.0

Major Scale          = 1.001

Minor Scale          = 0.999.

 Stretch only parameters would be as follows :-

Distortion Angle     = 21.0

Major Scale          = 1.002

Minor Scale          = 1.000

Corrected Pixel Size = 0.669

The Total Distortion = .15%

=========================================

Note that the values of both major and minor scale remind the same as before its corrected, but the distortion angle changed dramatically. Why could be the reason for this? If you had experience with the mag_distortion_estimate/correct, would you please let me know if there is anything that I should specifically pay attention to in order to get the accurate estimation?

Many thanks in advance.

Yuejiao Xian

Ph.D candidate,
Department of Chemistry and Biochemistry,
University of Texas at El Paso
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<https://urldefense.com/v3/__https://nam01.safelinks.protection.outlook.com/?url=https*3A*2F*2Fmail.ncmir.ucsd.edu*2Fmailman*2Flistinfo*2F3dem&data=01*7C01*7Cyxian*40miners.utep.edu*7Cbc4f87ac85e3459db20e08d84080c000*7C857c21d21a1643a490cfd57f3fab9d2f*7C1&sdata=u1X9XSlt0rNXEFYJVKys6NMuK7WfTQk3S0hbmcF9hr4*3D&reserved=0__;JSUlJSUlJSUlJSUlJQ!!Mih3wA!WMcSQN1PkD1WfwvzV1Kti07yAOu9coTxp-OvXxWLrcuzzuJoYVliRoSAll-FruQP_Q$ >
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/30d1717f/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 1583683 bytes
Desc: image.png
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200814/30d1717f/attachment-0001.png>