[3dem] Documentation on Difference Map tools

[Ludtke, Steven J.]

This reply from the EMAN2 mailing list shows how to do it in one line:

Hi Aaron, sorry you got me in transit, and I didn't catch up on my mail until today.

Difference maps are rarely useful due to differences in filtration, CTF correction, and other things. Usually other representations for visualizing differences between maps are preferred nowadays. If you really feel you must do a difference map, the strategy for doing it 'correctly' to the extent that's possible is:

e2proc3d.py <inputA> <output> --matchto <inputB> --mult -1 --addfile <inputB>


This strategy has been the standard in EMAN/EMAN2 for ~20 years. You match the power spectrum of one map to the other, then subtract. The differences have little enough impact on the power spectrum that as long as them maps are moderately similar this works fairly well. However, in most cases 'morphing' between the aligned maps provides a better visualization of the differences. Depends a bit on the purpose

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Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (https://urldefense.com/v3/__http://www.bcm.edu/biochem__;!!Mih3wA!Vq9wyA7Wmu8-hSWGxUzWL1NtpUPEV4OqWJ_zppeQ0GYI1n8JgPU4Ut66ZsTcDkDBvw$ <https://urldefense.com/v3/__http://www.bcm.edu/biochem__;!!Mih3wA!Vq9wyA7Wmu8-hSWGxUzWL1NtpUPEV4OqWJ_zppeQ0GYI1n8JgPU4Ut66ZsTcDkDBvw$ >)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<https://urldefense.com/v3/__http://cryoem.bcm.edu__;!!Mih3wA!Vq9wyA7Wmu8-hSWGxUzWL1NtpUPEV4OqWJ_zppeQ0GYI1n8JgPU4Ut66ZsShYimlFQ$ >)
Co-Director CIBR Center                                    (https://urldefense.com/v3/__http://www.bcm.edu/research/cibr__;!!Mih3wA!Vq9wyA7Wmu8-hSWGxUzWL1NtpUPEV4OqWJ_zppeQ0GYI1n8JgPU4Ut66ZsRRSAFEpQ$ <https://urldefense.com/v3/__http://www.bcm.edu/research/cibr__;!!Mih3wA!Vq9wyA7Wmu8-hSWGxUzWL1NtpUPEV4OqWJ_zppeQ0GYI1n8JgPU4Ut66ZsRRSAFEpQ$ >)



On Jul 28, 2020, at 12:28 PM, André Graça <andre.graca at umu.se<mailto:andre.graca at umu.se>> wrote:

***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
________________________________
Dear community,

I am struggling to find good resources and documentation about appropriate tools to generate and help to interpret difference maps.

I have only found a paper (J. Chem. Inf. Model. 2020, 60, 2552−2560) about the tool integrated in CCP-EM software suite, but I wish to find more information. It is generally something I miss from the courses or tutorials I participated in.

Can anyone recommend any literature?

Keep enjoy the Summer!
André Graça
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