Dear Tim, Thank you for your suggestion, it worked well for me! Best regards,
Christian Il giorno mar 18 mar 2025 alle ore 11:56 Tim Gruene <[email protected]> ha scritto: > 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/
