Yes, Dorothee is right. Don't turn off all the bulk solvent! That is not a polder map.
In refmac you want to use the keyword: solvent exclude DUM And then fill the space you want to have no bulk solvent with water atoms with residue ID "DUM" and perhaps occupancy set to zero, since you don't want them contributing to Fcalc. You might also want to turn off clashes for these dummy atoms using: vdwrestraints DUMM 0 or vdwrestraints exlcude documentation is here: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html Refmac also supports externally-defined solvent, which can be very handy. All you need is structure factors (amplitudes and phases) in the same MTZ file as your data. I like to call them Fsolvent PHIsolvent. Put these on the LABIN line with FPART1=Fsolvent PHIP1=PHIsolvent. You will probably also want to use: SCPART 1 Tells refmac to optimize the scale and B factor assigned to your bulk solvent. You probably also want: SOLVNET NO This turns off the built-in bulk solvent calculation. If you don't do this, refmac will scale its own default bulk solvent mask alongside your manually-provided mask. Then again, you might want to do that just to see what happens. In fact, you can provide refmac with several "partial structure" masks. All of them will get scaled if you put their number on the SCPART line. If you want the map that refmac uses by default, use the MSKOUT feature to have refmac write it out for you. You can then scale this map with mapmask to make sure it has a range from 0 to 1. You might also want to use other map masking tools on it. Once you have a solvent map you want to use, you can convert this map into structure factors using refmac's "mode sfcalc" feature. Also documented on the link above. Then you can provide them as FPART1 PHIP1 as above. -James Holton MAD Scientist On 2/4/2019 4:13 PM, Dorothee Liebschner wrote: Hi, Please note that for polder maps, the bulk solvent is reset locally. Turning bulk solvent off entirely most likely deteriorates maps. Best wishes, Dorothee On Mon, Feb 4, 2019 at 3:50 AM Samuel Davis (PG Research) <s.w.da...@dundee.ac.uk<mailto:s.w.da...@dundee.ac.uk>> wrote: Hi, I'm wondering if anyone knows if it is possible to turn off the bulk solvent modelling in Refmac5, for the purpose of generating Polder maps? I know that an option for Polder maps is directly implemented in Phenix, but we ideally want to use Refmac5, as we have used it for the rest of our refinement and want to keep it consistent if possible. Thanks, Samuel. Samuel Davis MRC 3.5 Year Programme PhD Student Life Sciences, Biological Chemistry and Drug Discovery, University of Dundee +44 (0)1382 388325 | swda...@dundee.ac.uk<mailto:swda...@dundee.ac.uk> Scottish University of the Year The Times / Sunday Times Good University Guide 2016 and 2017 Follow my blog: https://musingsofanearlycareerscientist.wordpress.com The University of Dundee is a registered Scottish Charity, No: SC015096 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org<https://phenix-online.org/> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
