Just for completeness: BUSTER includes an automatic so-called "void correction" that tries to detect those incorrectly bulk-solvent filled cavities and correct for it. Nothing for you to do extra, since that correction is on by default ... and works as expected in a lot of cases as far as we can tell. And yes, it is also approaching this in a "all or nothing" manner, so not very subtle.
Cheers Clemens PS: see also https://www.globalphasing.com/buster/ https://www.globalphasing.com/buster/wiki/index.cgi?BusterFAQ#abruptRchange https://www.ccp4.ac.uk/schools/DLS-2019/course_material/day7/Vonrhein_GlobalPhasing_BUSTER_CCP4-DLS2019.pdf On Sun, Jul 18, 2021 at 10:57:59AM -0700, James Holton wrote: > There are two ways to test the "too much bulk solvent" hypothesis. > > 1) examine the bulk solvent electron density map. > This is (IMHO) a lot harder than it should be, but here are two recipes: > refmac5 : on the command line, put "mskout rawmask.map" somewhere among > the hklin xyzin, etc directives. This will create a map you can load into > coot with the "File:Open map..." menu item. > phenix: use phenix.fmodel twice. Once with k_sol=1, and again with > k_sol=0. Load the two resulting mtz files into coot with "File:Open MTZ, > mmCIF, fcf or phs..." and then create a difference map between them using > "Calculate:Map Tools...:Make a Difference Map...". This difference map will > be the bulk solvent component. > > 2) suppress the bulk solvent. > The easiest way to do this is fill the region with water atoms at low > occupancy, such as 0.01. These will contribute essentially no electron > density of their own, but will also prevent the refinement program from > putting bulk solvent anywhere near them. At least with current algorithms, > atoms at any occupancy exclude 100% of bulk solvent. Since they will be > poorly restrained, you might want to fix these waters in place with harmonic > restraints, or otherwise tell your favorite refinement program to not move > them. Your documentation may vary. -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
