<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Asmahan,<div class=""><br class=""></div><div class=""> The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file. Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1.</div><div class=""><br class=""></div><div class=""><div class="">ATOM 1 N ASP B 1 -0.818 -36.026 -12.912 1.00 85.53 N </div><div class="">ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C </div><div class="">ATOM 3 C ASP B 1 0.706 -34.352 -13.882 1.00 85.53 C </div></div><div class=""><br class=""></div><div class=""><div>The bfactor is assigned to every atom. But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines.</div><div><br class=""></div><div><div>$ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb</div><div>ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C </div><div>ATOM 10 CA CYS B 2 1.983 -32.130 -13.721 1.00 95.45 C </div><div>ATOM 16 CA PRO B 3 3.029 -30.770 -17.151 1.00 93.20 C </div><div>ATOM 23 CA SER B 4 6.629 -31.094 -18.066 1.00 93.36 C </div><div class=""><br class=""></div><div class="">You can also write the values into a ChimeraX attribute file using ChimeraX commands</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>select #1@CA</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true</div><div class=""><br class=""></div><div class="">and that file looks like the following</div><div class=""><br class=""></div><div class=""><div class="">attribute: bfactor</div><div class="">recipient: atoms</div><div class="">match mode: 1-to-1</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>/A:1@CA<span class="Apple-tab-span" style="white-space:pre"> </span>56.150001525878906</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>/A:2@CA<span class="Apple-tab-span" style="white-space:pre"> </span>53.33000183105469</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>/A:3@CA<span class="Apple-tab-span" style="white-space:pre"> </span>53.59000015258789</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>/A:4@CA<span class="Apple-tab-span" style="white-space:pre"> </span>59.380001068115234</div></div><div class=""><br class=""></div><div class="">documentation here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes" class="">https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes</a></div><div class=""><br class=""></div></div><div> Tom</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <<a href="mailto:Asmahan.Alghamdi@nottingham.ac.uk" class="">Asmahan.Alghamdi@nottingham.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="elementToProof" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Dear Tom, </div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)? </div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Thank you very much.</div><div class="elementToProof ContentPasted0" style="font-style: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; background-color: rgb(255, 255, 255);">Asmahan </div></div></blockquote></div><br class=""></div></body></html>