On Tue, 18 Mar 2025 09:21:44 +0100 Christian Buratto <[email protected]> wrote:
> Dear CCP4 community, > I am currently trying to determine the structure of a > protein-polyoxometalate complex. I am using a polyoxometalate > molecule that is a derivative of the one deposited in the CCDC (ICSD: > 173439). I am facing difficulties in generating a restraint file for > this metal-oxo molecule that can be recognized by Phenix, both for > ReadySet and refinement jobs. I have attempted to use ACEdrg and > ELBOW, but all my trials have been unsuccessful. A common error in > refinement states that Phenix is unable to determine the energy type > for Ru or W atoms present in my ligand molecule. If anyone has any > suggestions or alternative approaches, I would greatly appreciate > your input! Thank you all for your time and help. > Best regards, > Christian > > ######################################################################## > > 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/ Dear Christian, sounds like a perfect task for the grade server, https://grade.globalphasing.org in combination of babel. Usually, I generate a PDB file (e.g. with PLATON or SHELXL), then use babel to convert to mol2 obabel -o mol2 -O yourligand.mol2 yourligand.pdb and upload the mol2-file to the grade server. This honours your atom naming. Make sure the PDB input file includes a residue name (which is easily done with SHELXL). Cheers, Tim -- -- 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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