To verify the presence of a non protein ligand, you need to come at this from an unbiased perspective.
1. Remove what you think is not there (e.g. disulfide bond) by truncating the Cys residues 2. Examine the difference density map to see if it conforms to your expectations of what is proposed to be there (or does not) 3. If appropriate, build and attach ligand and re-refine. I am assuming that you are proposing a thioketal adduct, which is not the same as inserting an acetone molecule in the structure. You can find generic instructions for these types of tasks on my XRD-protocols site, https://sites.google.com/colgate.edu/xrd-protocols. Roger Rowlett On Tue, Jun 30, 2020, 7:25 AM Daniele Veggi <veggidani...@gmail.com> wrote: > Hi Yadav, > yes, this is only a representation of what I would like to do. If during > the refinement will continue to appear density, probably I'm on the good > track......but currently my big issue is inserting the ACN > covalently linked to both cys. > > many thanks > > Daniele Veggi > GSK Vaccines Siena Italy > > > > > > Il giorno mar 30 giu 2020 alle ore 12:52 Lumbini Yadav < > lumbin...@gmail.com> ha scritto: > >> Hi Daniele, >> Do you see Fo-Fc density near disuphide bond where you are trying to fit >> acetone? >> >> On Tue, Jun 30, 2020 at 3:28 PM Daniele Veggi <veggidani...@gmail.com> >> wrote: >> >>> Dear CCP4bb, >>> >>> I'm trying to insert an Acetone molecule between two cysteine residues >>> in coot or modifying the pdb. I'm working on this modified molecule where >>> the disulfide bridge was chemichally opened and inserted an acetone >>> molecule between the two cysteine. >>> >>> MS data confirm this modification (98% of molecules modified) but I can >>> not insert the acetone covalently linked to the S of both cysteine >>> (S-ACN-S). >>> Maybe what I think and what I am doing is not the right solution (the >>> disulfide bridge is still alive?) anyway i would like to know how to link >>> the acetone to the two cysteine >>> To better understand what I mean in attach you find a screenshot >>> >>> I thank in advance all those who will have the courtesy to make a >>> suggestion >>> >>> Daniele Veggi >>> >>> ------------------------------ >>> >>> 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 > ######################################################################## 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/
