Dear all. Would it help to separate out the issue of the FSC from the value of the threshold? My understanding is that the FSC addresses the spatial frequency at which there is a reliable information content in the image. This concept should apply to a wide variety of types of image. The issue is then what value of the threshold to use. For interpretation of protein structures (whether by x-ray or electron microscopy), a half bit threshold appears to be appropriate. However, for imaging the human brain (one of Marin’s examples) a higher threshold might be adopted as a range of contrasts might be present (axons for example have a similar density to the surroundings). For crystallography, if one wants to see lighter atoms (hydrogens in the presence of uranium or in proteins) a higher threshold might also be appropriate. I am not sure about this to be honest as a 2 bit threshold (for example) would mean that there is information to higher resolution at a threshold of a half bit (unless one is at a diffraction or instrument limited resolution).
Most CCP4BBers will understand that a single number is not good enough. However, many users of the protein structure databases will simply search for the structure with the highest named resolution. It might be difficult to send these users to re-education camps. Regards Colin From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Petrus Zwart Sent: 16 February 2020 21:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [3dem] Which resolution? Hi All, How is the 'correct' resolution estimation related to the estimated error on some observed hydrogen bond length of interest, or an error on the estimated occupancy of a ligand or conformation or anything else that has structural significance? In crystallography, it isn't really (only in some very approximate fashion), and I doubt that in EM there is something to that effect. If you want to use the resolution to get a gut feeling on how your maps look and how your data behaves, it doesn't really matter what standard you use, as long as you are consistent in the use of the metric you use. If you want to use this estimate to get to uncertainties of model parameters, you better try something else. Regards Peter Zwart On Sun, Feb 16, 2020 at 8:38 AM Marin van Heel <0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk<mailto:0000057a89ab08a1-dmarc-requ...@jiscmail.ac.uk>> wrote: Dear Pawel and All others .... This 2010 review is - unfortunately - largely based on the flawed statistics I mentioned before, namely on the a priori assumption that the inner product of a signal vector and a noise vector are ZERO (an orthogonality assumption). The (Frank & Al-Ali 1975) paper we have refuted on a number of occasions (for example in 2005, and most recently in our BioRxiv paper) but you still take that as the correct relation between SNR and FRC (and you never cite the criticism...). Sorry Marin On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A <pawel.a.penc...@uth.tmc.edu<mailto:pawel.a.penc...@uth.tmc.edu>> wrote: Dear Teige, I am wondering whether you are familiar with Resolution measures in molecular electron microscopy. Penczek PA. Methods Enzymol. 2010. Citation Methods Enzymol. 2010;482:73-100. doi: 10.1016/S0076-6879(10)82003-8. You will find there answers to all questions you asked and much more. Regards, Pawel Penczek Regards, Pawel _______________________________________________ 3dem mailing list 3...@ncmir.ucsd.edu<mailto:3...@ncmir.ucsd.edu> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org<http://www.phenix-online.org/> CAMERA: http://camera.lbl.gov/ ------------------------------------------------------------------------- ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
