Dear Florian, I had a similar problem in the past. The uninterpretable electron density was mainly because of weird refinement of anisotropic ADPs. The resolution was about 1.2 AA. The refinement was somehow divergent. Is it also your case? You can check the ellipsoidal ADPs in Coot. Moreover, do you leave REFMAC to decide on twinning or do you force the twin law and fix fractions by a command? This could also make a difference. Best regards, Petr ________________________________________ From: CCP4 bulletin board <[email protected]> on behalf of Schubot, Florian <[email protected]> Sent: Monday, September 26, 2022 5:14:01 PM To: [email protected] Subject: Re: [ccp4bb] Strange crystal packing in twined crystal -follow up
Dear all, A couple of months ago I posted a message about strange crystal packing to the bb. Thank you all for your insightful responses. When we were unable to find any spurious electron density in the gap, we wondered if perhaps the twinning caused us to impose too high symmetry on our data (and structure). So, we reindexed and reprocessed our data in P1 and later P2 (originally C2). That did the trick. Now the molecular replacement solution has completely normal packing and the Rfree has fallen below .30. Interestingly, applying the twin law suggested by Xtriage during refinement substantially improves the stats but the map is uninterpretable, while the untreated data yield beautiful maps. Anyway, I thought this is a nice contribution to "pathological crystallography". Florian ========================================================= Florian Schubot, Ph.D. Associate Professor Virginia Polytechnic Institute and State University Department of Biological Sciences 5002 Derring Hall 926 West Campus Dr Blacksburg, VA 24061 United States E-mail: [email protected] Phone: (540) 231-2393 Fax: (540) 231.4043 http://www.faculty.biol.vt.edu/schubot/ ========================================================= ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Caaleshin%40SBPDISCOVERY.ORG%7Cdf30ff99fe834fd64ae708da6b471374%7C0b162723004547deb0699f1a7aa955a1%7C0%7C1%7C637940250285850378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=pw6cjSGGlGJzWBlq7UFmvtxpwfehJKoH8sgdCJxYlrA%3D&reserved=0> ________________________________ 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/
