[3dem] deposition of half maps

[Ludtke, Steven J.]

Hi David,
people proposed making deposition of 1/2 maps mandatory at various EMDB meetings in the past. The issue is that some software uses other mechanisms for determining resolution, so the half maps do not always exist. So they became 'strongly encouraged' but not required. Similarly, the filtration applied to final maps is often a lot more complicated than a simple Gaussian B-factor. Even the concept of "unfiltered, unmasked" maps is quite ambiguous, since each software package will have a different mathematical concept of "unfiltered and unmasked", and in many strategies completely unmasked unfiltered volumes cannot be produced.


--------------------------------------------------------------------------------------
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                      (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<http://cryoem.bcm.edu>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)



On Mar 27, 2020, at 11:21 AM, David Stokes <stokes at nyu.edu<mailto:stokes at nyu.edu>> wrote:

Sorry, I take it back. I just encountered an entry in EMDB with half maps available.
So I guess it is an optional upload, which I would encourage everyone to do.

Keep safe everyone.
David


On 3/27/2020 12:11 PM, David Stokes wrote:
I have been downloading maps from the EMDB for inspection.
I want to play with the temperature factor to follow up on proposals to identify charged ligands
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1107_S2052252518006292&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=BvMPM98arHCRPl6_9PFNx7tqCtS2VBcOA-KEpqCoZG4&s=1pi2uoHT84L_P5dIf_0ycwPEjhTYNQLqjh8p8_fqTOk&e= However, I don't see any information about temperature factor used to generate the maps in the EMDB metadata and there is no evidence of half map desposition, which would allow me to investigate various map manipulation tricks (e.g., different B factors & phenix density modification).

Should I be looking somewhere else for this data or has our discussion on this topic been a lot of hot air?

David


_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=BvMPM98arHCRPl6_9PFNx7tqCtS2VBcOA-KEpqCoZG4&s=Bwdvvhr8z3Rra7WfdQOMnUv_oWZTSXnTyXOirfV34wE&e=

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20200327/f2efe07b/attachment-0001.html>