<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="">Hi Winston,<div class=""><br class=""></div><div class=""> The command would look like</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>open /Users/jin/data/myfile.mtz structure #1</div><div class=""><br class=""></div><div class="">where #1 is the id number of the PDB structure that you have already opened -- the correct number will be listed in the Models panel in ChimeraX. Each model you open gets a number starting at 1.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 22, 2021, at 10:06 AM, Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Tristan,</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks a lot for your help!<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I have installed your ISOLDE in ChimeraX, and was able to load the mtz file using the “</span><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">Load crystallographic dataset" button on ISOLDE's GUI.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(47, 85, 151);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(47, 85, 151);" class="">I will try<span class="Apple-converted-space"> </span></span><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(47, 85, 151);" class="">"open filename.mtz structureModel #{model id}" after I am more familiar with the file path syntax in ChimeraX.<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best wishes,</span><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><br class=""><br class="">Winston<br class=""><br class=""></span><span lang="EN-US" style="font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><div class=""><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(225, 225, 225); padding: 3pt 0cm 0cm;" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>Tristan Croll [<a href="mailto:tic20@cam.ac.uk" class="">mailto:tic20@cam.ac.uk</a>]<span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, June 23, 2021 12:27 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>; Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw" class="">winston@gate.sinica.edu.tw</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] Open a PDB-formatted file and a MTZ file<o:p class=""></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" class=""><o:p class=""> </o:p></span></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">Hi Winston,<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">The failure to open a MTZ file properly via the File/Open GUI is my fault, and something I'll be remedying with the next release of ISOLDE/Clipper. For now, you can do it at the command line using "open filename.mtz structureModel #{model id}", or via the "Load crystallographic dataset" button on ISOLDE's GUI.<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></span></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">Best regards,<o:p class=""></o:p></span></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" style="font-family: Calibri, sans-serif;" class="">Tristan<o:p class=""></o:p></span></div></div><div class="MsoNormal" align="center" style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif; text-align: center;"><span lang="EN-US" class=""><hr size="2" width="98%" align="center" class=""></span></div><div id="divRplyFwdMsg" class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users-bounces@cgl.ucsf.edu</a>> on behalf of Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>22 June 2021 17:14<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[chimerax-users] Open a PDB-formatted file and a MTZ file</span><span lang="EN-US" class=""><o:p class=""></o:p></span></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div></div></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">Hi,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I am trying to inspect electron density of X-ray data.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz).<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I have downloaded Clipper to Chimera X (1.2.5) running on Window 10.<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I have opened my a.pdb, and I then tried to open my a.mtz file from the File-Open and I specified the file type with “*.mtz”, and opened the a.mtz file, but I then got the error message: “Must specify a structure model to associate with crystallographic data”.<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class="">I know that I was not doing it correctly (e.g. not typing proper commands with correct syntax.). I looked into the description in the URL below. However, I just could not get it work. Any help will be appreciated. Thanks!<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""><a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper</a><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span lang="EN-US" class=""> <o:p class=""></o:p></span></div><p class="xmsonormal" style="margin: 0cm 0cm 12pt; font-size: 12pt; font-family: Calibri, sans-serif;"><span lang="EN-US" class="">Best wishes,<br class=""><br class="">Winston<o:p class=""></o:p></span></p></div></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 12px; 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: 12px; 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="">ChimeraX-users mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 12px; 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=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a></span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 12px; 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="">Manage subscription:</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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: 12px; 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=""><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span></div></blockquote></div><br class=""></div></body></html>