Hi Manjula, For the 1) I would use first AVOGADRO to design the peptide and then run an energy minimization. Next, I would run eLBOW in PHENIX to generate the .cif file (constraints) that you need to import in COOT to allow for the real-space refine (otherwise it will stay a stick).
To the 2) I would say “with a lot of try and error and patience” but I guess that this applies to crystallography in general. Also, by the shape of your positive density, could it be possible for it to be 2 molecules of this peptide? Hope this helps. Cheers, Nikolas On Thu, 27 Feb 2025 at 16:10, Manjula Ramu <manjula....@gmail.com> wrote: > Dear all, > > I recently solved a complex structure of a protein with an 11-amino-acid > phosphopeptide at 2.58 Å resolution. The asymmetric unit contains two > protein chains, and the difference map shows positive green density (Fo-Fc > positive difference density) for the peptide. However, the density is not > well-defined, making manual fitting of the peptide challenging. > > I have two key questions: > > 1. *How can I generate a 3D model of the 11-residue phosphopeptide?* > 2. *What options are available for fitting the peptide into the > electron density?* > > I would greatly appreciate any guidance or suggestions to help complete my > structure. I have attached the png file from the coot. > > ---------------------------------------------------- > > Thanks and Regards, > > *Manjula * > > > > > > <https://www.nimhans.kar.nic.in/> > > ------------------------------ > > 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/
