Mitch, For discernment of Sodium versus Potassium, you could also look at the bonding distances and coordination of the metal present. Ran into this problem back in the day. Check out Figure 6 C,D in the following pub:
https://pubs.acs.org/doi/10.1021/bi060653d Scott -- Scott Pegan Professor Division of Biomedical Sciences School of Medicine University of California Riverside 205 SOM Research Building 900 University Avenue Riverside, CA 92521-0001 (951) 827 7907 sco...@medsch.ucr.edu On 9/8/22, 9:51 AM, "CCP4 bulletin board on behalf of Mitchell D. Miller" <CCP4BB@JISCMAIL.AC.UK on behalf of mitchell.d.mil...@rice.edu> wrote: You can also look at your anomalous maps. For most energies/wavelengths used to collect protein data, f" for K will be just under 2x the f" for S while for Na f" will be much less (0.2-0.25 of S). So you can use S atom anomalous as an internal reference. If you see anomalous peaks at your S atoms, then you would also expect peaks at K atoms but not at Na atoms. Regards, Mitch $ echo 'Atom Wave (keV) f"' ; for atom in NA S K ; do echo -e NWAV 5 0.9 1 1.2 1.4 1.7"\n"ATOM $atom"\nEND\n"| crossec | awk 'NF==4&&$2+1>1{printf "%3s %6.2f %6.2f %8.4f\n", $1, $2, 12.39842/$2, $4}'; done | sort -k2,2n -k4n Atom Wave (keV) f" NA 0.90 13.78 0.0411 S 0.90 13.78 0.1982 K 0.90 13.78 0.3948 NA 1.00 12.40 0.0512 S 1.00 12.40 0.2439 K 1.00 12.40 0.4819 NA 1.20 10.33 0.0746 S 1.20 10.33 0.3474 K 1.20 10.33 0.6770 NA 1.40 8.86 0.1023 S 1.40 8.86 0.4656 K 1.40 8.86 0.8979 NA 1.70 7.29 0.1507 S 1.70 7.29 0.6677 K 1.70 7.29 1.2685 Quoting Eleanor Dodson <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>: > Is that the right way round? Atomic no K 19, Na 11 > > Call something K when it should be NA - B factor will shoot to reduce the > atom contribution. > Call something Na when it should be K - B factor will become very small.. > > As you say - check which fits best with the surrounding atoms.. > > > > On Thu, 8 Sept 2022 at 14:16, Jon Cooper < > 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Hello, K will always have a higher B-factor for a given piece of density >> due to it having a larger atomic number. Is the K B-factor much higher than >> those of neighbouring atoms and, if not, it's probably the best >> interpretation? Cheers, Jon.C. >> >> >> Sent from ProtonMail mobile >> >> >> >> -------- Original Message -------- >> On 8 Sep 2022, 14:07, smita yadav < sm...@rcb.res.in> wrote: >> >> >> Dear Community, >> Can you tell me. if we fit some metal in X-ray >> structure and its geometry and other properties are satisfied but showing >> some higher B-factor. does it validate to put that metal-ligand.ligand. At >> one site 2 metals such as K and NA fit, but K shows a higher B-factor, but >> other parameters such as geometry and other fit better for K instead of NA. >> So, out of the two ligands at the same site which one would be more >> favorable to be fit. >> -- >> >> On Thu, Sep 8, 2022 at 6:35 PM smita yadav <sm...@rcb.res.in> wrote: >> >>> >>> Dear Community, >>> Can you tell me. if we fit some metal in X-ray >>> structure and its geometry and other properties are satisfied but showing >>> some higher B-factor. does it validate to put that metal-ligand.ligand. At >>> one site 2 metal such as K and NA fits, but K shows higher >>> -- >>> Regards, >>> Smita Yadav >>> Ph.D SRF >>> Regional Centre for biotechnology, >>> Haryana-121001. >>> >> >> >> -- >> Regards, >> Smita Yadav >> Ph.D SRF >> Regional Centre for biotechnology, >> Haryana-121001. >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGp3IzHaXM$ >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGp3IzHaXM$ >> >> > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGp3IzHaXM$ > > This message was issued to members of > https://urldefense.com/v3/__http://www.jiscmail.ac.uk/CCP4BB__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGpYf6GO4Y$ , a mailing list hosted by https://urldefense.com/v3/__http://www.jiscmail.ac.uk__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGpGhzi6iA$ , terms & conditions are available at > https://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!BuQPrrmRaQ!j4Jxm8G7hxgiQ78SgXRomsl3jV7CN_HWdspxFjnB6yYaOvsidHDmMGB7EqhyNU5IsutXabxeu82bc3FbfrRCjxL1Y8k8w_Nt6qGpuizNqfc$ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!OLyWHuc!X1UOVT_JtoU3qZOvK1MG7Y5Vs_p4GtCdDN1-OMXtOxBulpeLu1UPKXt7kRFlLLMzOnqg3mRoo5fHu2VejaH6Tc_7U3m8vyoke6mg$ 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://urldefense.com/v3/__https://www.jiscmail.ac.uk/policyandsecurity/__;!!OLyWHuc!X1UOVT_JtoU3qZOvK1MG7Y5Vs_p4GtCdDN1-OMXtOxBulpeLu1UPKXt7kRFlLLMzOnqg3mRoo5fHu2VejaH6Tc_7U3m8v7YFkXvi$ ######################################################################## 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/
