<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Thanks for chiming in Randy. We could consider reindexing.</div><div class="">The goal is to update the entry in such a way that “round trip” refinement becomes possible using modern software.</div><div class="">Phenix is not the only program that cannot handle “A 1”.</div><div class="">Can you suggest software that can assist in identifying reindexing strategy for merged amplitudes?</div><div class=""><br class=""><div class=""><div class=""><div class="">
<div><br class=""><blockquote type="cite" class=""><div class="">On Dec 14, 2022, at 15:50, Randy John Read <<a href="mailto:rjr27@cam.ac.uk" class="">rjr27@cam.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Hi Cathy,</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Presumably you’re trying to keep the original cell, which is why you haven’t reindexed to a smaller P1 cell?</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">We’ve run into this problem when we wanted to test whether pseudo-centering in a P1 crystal was really a centering operator. Is that what you’re trying to do? If so, I can’t help because we gave up and just reindexed!</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Randy</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><blockquote type="cite" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">On 14 Dec 2022, at 16:49, Cathy Lawson <<a href="mailto:cathy.lawson@rcsb.org" class="">cathy.lawson@rcsb.org</a>> wrote:<br class=""><br class="">Thanks Pavel.<br class=""><br class="">I tried adding _struct_ncs_oper matrices to the input cif file but got a phenix error that an identity rotation with non-zero translation elements was improper.<span class="Apple-converted-space"> </span><br class="">It would be great if the code could be modified to accept this transformation.<br class=""><br class=""><blockquote type="cite" class="">On Dec 14, 2022, at 11:25, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>> wrote:<br class=""><br class="">Hi Cathy,<br class=""><br class="">making the 2nd copy and working in P1 seems as fine option to me. And no, cctbx doesn't know A1.<br class=""><br class="">If this is for refinement you can use NCS constrains which will enforce the strict symmetry on everything: coordinates, occupancies, B factors.<br class=""><br class="">Pavel<br class=""><br class=""><br class="">On 12/14/22 07:31, Cathy Lawson wrote:<br class=""><blockquote type="cite" class="">Looking for suggestions — cctbx/phenix seems not to be able to handle a triclinic lattice with centering.<br class=""><br class="">Specific Example: PDB entry 1LKS with cell parameters/space group “A 1”: CRYST1 31.970 65.080 27.250 94.57 111.56 82.98 A 1 2<br class=""><br class="">A 1 diagram:<span class="Apple-converted-space"> </span><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimg.chem.ucl.ac.uk%2Fsgp%2Flarge%2F001bz1.htm&data=05%7C01%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C27a6359621024bb8b37208daddf37afd%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638066335049293047%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VvbkrtwH9AdH1irFnag8F4vCnMfDVib%2F%2B7VutLIVdmw%3D&reserved=0" class="">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimg.chem.ucl.ac.uk%2Fsgp%2Flarge%2F001bz1.htm&data=05%7C01%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C27a6359621024bb8b37208daddf37afd%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638066335049293047%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VvbkrtwH9AdH1irFnag8F4vCnMfDVib%2F%2B7VutLIVdmw%3D&reserved=0</a><br class=""><br class="">Are there any other options for working with this data in phenix other than creating an explicit 2nd copy of the coordinates at x, 1/2+y,1/2+z and setting space group to primitive lattice P 1?<br class=""><br class="">Thanks in advance.<br class=""></blockquote></blockquote><br class=""><br class="">_______________________________________________<br class="">phenixbb mailing list<br class=""><a href="mailto:phenixbb@phenix-online.org" class="">phenixbb@phenix-online.org</a><br class=""><a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fmailman%2Flistinfo%2Fphenixbb&data=05%7C01%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C27a6359621024bb8b37208daddf37afd%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638066335049293047%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rW3w%2B0WeGnVKCp6OnbNCGisMm%2FedNzI7XR2GUjW31nM%3D&reserved=0" class="">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fphenix-online.org%2Fmailman%2Flistinfo%2Fphenixbb&data=05%7C01%7Crjr27%40universityofcambridgecloud.onmicrosoft.com%7C27a6359621024bb8b37208daddf37afd%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638066335049293047%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=rW3w%2B0WeGnVKCp6OnbNCGisMm%2FedNzI7XR2GUjW31nM%3D&reserved=0</a><br class="">Unsubscribe:<span class="Apple-converted-space"> </span><a href="mailto:phenixbb-leave@phenix-online.org" class="">phenixbb-leave@phenix-online.org</a><br class=""></blockquote><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">-----</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Randy J. Read</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Department of Haematology, University of Cambridge</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Cambridge Institute for Medical Research Tel: +44 1223 336500</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">The Keith Peters Building Fax: +44 1223 336827</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Hills Road E-mail:<span class="Apple-converted-space"> </span></span><a href="mailto:rjr27@cam.ac.uk" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">rjr27@cam.ac.uk</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; 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; float: none; display: inline !important;" class="">Cambridge CB2 0XY, U.K. </span><a href="http://www-structmed.cimr.cam.ac.uk/" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">www-structmed.cimr.cam.ac.uk</a></div></blockquote></div><br class=""></div></div></div></div></body></html>