<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Phenix Developers/Users,<div class=""><br class=""></div><div class="">I have a question regarding how to generate a correct restrain for a whole nonstandard peptide and how do run refinement correctly.</div><div class=""><br class=""></div><div class="">The nonstandard peptide in my structure is pepstatin A (IVA Val Val STA Ala STA).</div><div class=""><br class=""></div><div class="">I manually put the pepstatin A in the density and generated the cif files for IVA and STA and run the refinement with them. </div><div class=""><br class=""></div><div class="">After refinement, the whole pepstatin A explored as pieces, which I guess the program treated the pepstatin A as single amino acids. </div><div class=""><br class=""></div><div class="">By the way, I also manual input the “LINK” information in the input pdb file as below,</div><div class=""><br class=""></div><div class=""><div class="">LINK C VAL L 3 N STA L 4 1555 1555 </div><div class="">LINK N ALA L 5 C STA L 4 1555 1555 </div><div class="">LINK C ALA L 5 N STA L 6 1555 1555</div></div><div class=""><br class=""></div><div class="">And also, when I use the “Real Space Refine Zone” by clicking two atoms for the whole pepstatin A in coot, it exploded again, although I input the same cif file in coot as well.</div><div class=""><br class=""></div><div class="">The data quality is not good (2.9 A with CC1/2=12), thus it is difficult to place amino acid individually to fit the destiny.</div><div class=""><br class=""></div><div class="">In the PDB, there are several structures containing the pepstatin A, such as 4TVG, 4AUC. They have the pepatatin A sequence as VVVXAX, but none of them lists the constrains.</div><div class=""><br class=""></div><div class="">Would you please help me and let me know how can I continue with refinement? Please let me know if you need more information.</div><div class=""><br class=""></div><div class="">Thank you vey much!</div><div class=""><br class=""></div><div class="">Yufan Wu</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; 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word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><font color="#999999" class="">Regards,</font></span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><font color="#999999" class=""><br class=""></font></span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><font color="#999999" class="">Yufan Wu</font><br class=""></span></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-family: arial, sans-serif; font-size: 13px; border-collapse: collapse;" class=""><font color="#999999" class="">The Plueckthun Lab</font></span></div><div style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="orphans: auto; widows: auto;" class=""><a href="http://www.bioc.uzh.ch/plueckthun" x-apple-data-detectors="true" x-apple-data-detectors-type="link" x-apple-data-detectors-result="0" class="">www.bioc.uzh.ch/plueckthun</a></div><span style="color: rgb(0, 0, 0); font-family: arial, sans-serif; font-size: 13px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; border-collapse: collapse;" class=""><font color="#999999" class="">Phone: +41 44 635 5574</font></span><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; 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