This doesn’t surprise me in the slightest, given what how the two maps are calculated.
The polder map is essentially the same as your "simple omit map” without the bulk solvent contribution that is present in the omit-refine map. Since this is an approximately constant contribution, if you recontour the Polder map to a higher contour you should be able to get the two maps to look basically the same. Nick On 23 Mar 2021, at 09:36, Sam Tang <samtys0...@gmail.com<mailto:samtys0...@gmail.com>> wrote: Dear colleagues Thanks a lot for the comments. I echo that this pentagon-like density may likely be water molecules. What had puzzled us a bit was that the output of Polder map which gave some interlinked density. I should also mention that this site is close to a predicted peptide binding site and that is what we are actually looking for. (To me the strong positive density in Polder map is not indicative of an amino acid residue as well.) My Polder map looks like this: https://drive.google.com/file/d/10dGpdcDhrp_ld6wPH3Er7iZ3KVgU2RCN/view?usp=sharing BRS Sam On Tue, 23 Mar 2021 at 04:43, Bernhard Rupp <hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> wrote: Textbook knowledge 😊 http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-28.htm ------------------------------------------------------ Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org<mailto:b...@hofkristallamt.org> +1 925 209 7429 +43 676 571 0536 --------------------------------------------------------- Doors and corners – that’s where they get you --------------------------------------------------------- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Sharan Karade Sent: Monday, March 22, 2021 13:10 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] unknown density Hi Please look at the pic attached. found similar pentagon water network. <image001.png> On Mon, Mar 22, 2021 at 12:40 PM Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: Definitely water pentamer, no doubt at all ;-0 Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 22 Mar 2021, 14:16, Mark J. van Raaij < mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>> wrote: The ring looks too big to be imidazole or a nucleotide or a carbohydrate, so it’s probably mainly water molecules. Perhaps partially replaced by PEG to explain the density between them (i.e. water molecules in most copies of the protein and PEG in some other copies). I’ve seen horse-shoe shaped PEG in a high-res structure before, PEGs in several confirmations might explain a circle. Practically speaking, I’d first model five waters and see if they refine well. Mark On 22 Mar 2021, at 14:58, Sam Tang <samtys0...@gmail.com<mailto:samtys0...@gmail.com>> wrote: Hello fellow colleagues Hope you are all well while the pandemics persists. I just wonder if anyone may have an idea what this density (looking like a pentagon) might be. The data was collected to 1.8 A and crystal was grown in Bis-tris + PEG3350. Imidazole residual? Nucleotide (the protein itself is nucleotide-binding, but shouldn't be at this particular site)? https://drive.google.com/file/d/1L9UBFmW72P214itM2HJR_DVy3FaA6FEZ/view?usp=sharing Thanks! BRS Sam ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Sharan Karade Postdoc-fellow IBBR-UMD, 9600 Gudelsky Dr, Rockville Maryland 20850 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
