Hi Manjula, It seems that you have a two fold symmetry axis, so surely you have two copies of the same peptide, building with the symmetric molecule on could help
HTH Daniele On Thu 27 Feb 2025 at 23:10, Nikolas <nikolas.ca...@gmail.com> wrote: > 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 > ######################################################################## 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/
