Hi It looks like the peptide is bound close to a 2_fold symmetry axis, which can result in mistakes, so try to anchor your peptide registry using regions that are away from this axis (turn symmetry on in COOT to make sure you dont build it inside itself).
Other than, that its just a case of treating it like any other part of a protein that needs rebuilding, and just apply the same iterative process where you improve/rebuild the bits you can, and as the maps improve The more difficult areas become more tractable. Some of the regions at the top-left of your image look like they may need rebuilding for instance, and once you have improved the protein, the peptide density may become more interpretable. The shape of the phosphate should hopefully be visible to help you. Once the protein part is as good as you think you can manage (and you have checked some of the weaker areas for model bias in the maps), then you can attempt to recover some of the finer details of your peptide. I personally use Polders or Phenix FEM maps. FEM maps can be really good. I'm not an expert in how they work, but personally I feel like the results are quite dependant on the quality of the phases you start with, so I usually use them To try and recover weak sidechain/ligand information in otherwise fairly complete models. Finally, once you think you have built your peptide you can add the phosphorylated residue which is (hopefully) in the existing dictionary using the "replace residue" tool in Coot I think. Hope this helps Matthew. ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Manjula Ramu <manjula....@gmail.com> Sent: 27 February 2025 21:09 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] unable to fit the 11-amino-acid peptide 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 ZjQcmQRYFpfptBannerStart This Message Is From a New External Sender You have not previously corresponded with this sender. Please exercise caution when opening links or attachments included in this message. ZjQcmQRYFpfptBannerEnd 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 [nimhans.kar.nic.in]<https://urldefense.com/v3/__https://www.nimhans.kar.nic.in/__;!!PDiH4ENfjr2_Jw!GlkzxGvMe_eiZpDRUY_r3AEaeFGjUWVyEHXwmOcBkPOiRrPU_jTyjsOW68L8MlQ9itm9gN74_1FCvE8DsmGkkdHAr0pAx7wN6K7qSg$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [jiscmail.ac.uk]<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!GlkzxGvMe_eiZpDRUY_r3AEaeFGjUWVyEHXwmOcBkPOiRrPU_jTyjsOW68L8MlQ9itm9gN74_1FCvE8DsmGkkdHAr0pAx7z24dSIxg$> ######################################################################## 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/
