Hi David, hi Roberto, ligands don't take classes on crystallography, and when there is space, they won't care about the symmetry of the main structure. Unless the ligand is very large, or includes heavy atoms, the intensities will not be disturbed very much by the ligand, and the symmetry determination will be dominated by the protein. You are lucky to see two conformations, in the worst case the ligand could be disordered and thus not visible. If you break the symmetry, you just double the work for the protein molecules (and may even destabilise the refinement), while the second molecule will most likely be the same within errors. Thus modelling two conformations for the ligand is a reasonable approach.
Best, Tim On Wed, 30 Jul 2025 09:56:13 +0000 David Briggs <[email protected]> wrote: > Hi Roberto, > > If I encountered that, I'd be thinking that the ligand violates the > space group symmetry, and therefore I'd drop that symmetry element > and reprocess the data in a lower sub-group and re-analyse. > > Zanuda would be helpful in the first instance. > > If this isn't your data/structure - I would hope that the authors may > discuss this observation in more detail the accompanying paper > > HTH. > > Dave > > > -- > > Dr David C. Briggs CSci MRSB (he/him) > > Principal Laboratory Research Scientist (Signalling and Structural > Biology Lab) > > and Co-chair, Crick Staff Consultative Forum > > The Francis Crick Institute > > London, UK > > Working hours: Mon-Fri 0900-1700 > > == > > about.me/david_briggs<https://about.me/david_briggs> | > OrcID<https://orcid.org/0000-0002-9793-7339> | Google Scholar > <https://scholar.google.co.uk/citations?user=DRKG5KwAAAAJ> > > == > > "Would it not be better if one could really 'see' whether > molecules...were just as experiments suggested?" > > – Dorothy Hodgkin > > ________________________________ > From: CCP4 bulletin board <[email protected]> on behalf of > Roberto Battistutta <[email protected]> Sent: 30 July 2025 > 10:50 To: [email protected] <[email protected]> > Subject: [ccp4bb] Ligand on a crystallographic axis > > > External Sender: Use caution. > > > Dear all, > > I'm puzzled by a structure in which a ligand is positioned on a > crystallographic axis (with occupancy 0.5) such that its symmetric > molecule is superimposed but inverted (see below). Any explanation as > to how this is possible? > > Thank you, > > Roberto. > > > ######################################################################## > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > [cid:[email protected]] > > > Roberto Battistutta > Associate Professor > Department of Chemical Sciences > University of Padua > via Marzolo 1, 35131 Padova - ITALY > tel. +39.049.827.5262 > fax. +39.049.827.5829 > [email protected] > > > ######################################################################## > > 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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > > The Francis Crick Institute Limited is a registered charity in > England and Wales no. 1140062 and a company registered in England and > Wales no. 06885462, with its registered office at 1 Midland Road > London NW1 1AT > > ######################################################################## > > 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/ -- -- Tim Gruene Head of the Core Facility Crystal Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 https://ccsa.univie.ac.at GPG Key ID = A46BEE1A ######################################################################## 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/
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