If you want to know what EDS does, read here http://eds.bmc.uu.se/eds/eds_help.html#NITTY_GRITTY
It does, indeed, run refmac to get bulk solvent and anisotropy corrections. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Alejandro Buschiazzo <[email protected]> </div><div>Date:05/27/2014 6:49 PM (GMT-05:00) </div><div>To: [email protected] </div><div>Subject: Re: Structure factors to CCP4 maps </div><div> </div>you're absolutely right. (mostly so, given these are questions to the coot bb :) ) Just one comment, and one question, if I may: 1.Comment: sometimes it's just a good idea to know what are you actually calculating, so a bit better to dig deeper in the files that you use, and get to the point where you need to choose for instance which coefficients to use etc. Especially for beginners (e.g. bad idea to look at a [Fcalc;PHIcalc] map...the map will look gorgeous ;) so on and so forth) 2. Actually this example is interesting, to learn a bit more about what is it that Coot is actually doing when invoking File -> Fetch PDB & Map using EDS It works indeed fine. If I go to EDS however, because of too high a disagreement on Rfactors, it actually doesn't enable me to get anything at all (am I missing something here?) And, going to "the source", in the PDB entry 1C75, the deposited structure factor file, only includes observed amplitudes (and sd's) for measured reflections. My question: closing coot after fetching the EDS entry (coot IS able to get something from EDS!?), if you look at the coot-download dir, you can find an mtz with many columns, including sigmaA-weighted amplitudes and phases for 2fo-fc anf fo-fc fourier ("a la Refmac") so, as Ed suggested, I guess coot is performing a 0 cycles refmac behind the scenes? or is it doing something else? wouldn't it be good to have also the original sf file saved in the download directory? thanks ale On 5/27/14, 19:07, Bernhard Lechtenberg wrote: Hi all, I might be missing something here, but in Coot, can you not just use File -> Fetch PDB & Map using EDS… to get both the model and the map? This definitely works for me for your example 1C75. Bernhard Bernhard C. Lechtenberg, PhD Postdoctoral Fellow Riedl Lab Sanford-Burnham Medical Research Institute 10901 North Torrey Pines Road La Jolla, CA 92037, USA Phone: 858.646.3100 x 4216 Email: [email protected] -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf
