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</o:shapelayout></xml><![endif]--></head><body lang=ZH-TW link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Hi Tom,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Thank you very much for testing this. <o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>It works now! (I must’ve done something wrong in renaming my files)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Hi Eric,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Thanks a lot! Your suggested command of “open browse struct #1” works well. It is not only handy but also necessary when accessing a folder (my) with its file name containing a space.<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Best wishes,</span><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><br><br>Winston<br><br></span><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'><o:p></o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> Tom Goddard [mailto:goddard@sonic.net] <br><b>Sent:</b> Wednesday, June 23, 2021 3:35 AM<br><b>To:</b> Wen-Jin Winston Wu <winston@gate.sinica.edu.tw><br><b>Cc:</b> chimerax-users@cgl.ucsf.edu<br><b>Subject:</b> Re: [chimerax-users] Open a PDB-formatted file and a MTZ file<o:p></o:p></span></p></div></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US>Hi Winston,<o:p></o:p></span></p><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>I just tested your open command putting an mtz file at D:\ttp.mtz and it worked fine in ChimeraX 1.2.5 with Clipper 0.16 on Windows 10<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US> open D:\ttp.mtz structure #1<o:p></o:p></span></p><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>If I type the wrong file name I do get the "No such file/path" message but if the file is there it works fine for me.<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US> </span></span><span lang=EN-US>Tom<o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US><br><br><o:p></o:p></span></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal><span lang=EN-US>On Jun 22, 2021, at 10:37 AM, Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></span></p></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Thanks Tom,</span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'> </span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>A silly question: my file is in my folder D under MS Windows (D:\).</span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>How do I open it with the command line?</span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>I’ve tried “open D:\ttp.mtz structure #1” , but it showed “</span><span lang=EN-US style='font-family:"Times New Roman",serif;color:#2F5597'>No such file/path: D:\ttp.mtz”</span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'> </span><span lang=EN-US><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Best wishes,<br><br>Winston<br><br><br></span><span lang=EN-US><o:p></o:p></span></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Tom Goddard [<a href="mailto:goddard@sonic.net">mailto:goddard@sonic.net</a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Wednesday, June 23, 2021 1:17 AM<br><b>To:</b><span class=apple-converted-space> </span>Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw">winston@gate.sinica.edu.tw</a>><br><b>Cc:</b><span class=apple-converted-space> </span>Tristan Croll <<a href="mailto:tic20@cam.ac.uk">tic20@cam.ac.uk</a>>; <a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [chimerax-users] Open a PDB-formatted file and a MTZ file</span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US>Hi Winston,<o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US> The command would look like<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US> </span></span><span class=apple-converted-space><span lang=EN-US> </span></span><span lang=EN-US>open /Users/jin/data/myfile.mtz structure #1<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US>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.<o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span class=apple-tab-span><span lang=EN-US> </span></span><span class=apple-converted-space><span lang=EN-US> </span></span><span lang=EN-US>Tom<o:p></o:p></span></p></div><div><div><p class=MsoNormal><span lang=EN-US><br><br><br><o:p></o:p></span></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal><span lang=EN-US>On Jun 22, 2021, at 10:06 AM, Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>> wrote:<o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Hi Tristan,</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Thanks a lot for your help!</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>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'>Load crystallographic dataset" button on ISOLDE's GUI.</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#2F5597'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#2F5597'>I will try<span class=apple-converted-space> </span>"open filename.mtz structureModel #{model id}" after I am more familiar with the file path syntax in ChimeraX.<span class=apple-converted-space> </span></span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif;color:#1F497D'>Best wishes,<br><br>Winston<br><br><br><br></span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><div><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>Tristan Croll [<a href="mailto:tic20@cam.ac.uk"><span style='color:purple'>mailto:tic20@cam.ac.uk</span></a>]<span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Wednesday, June 23, 2021 12:27 AM<br><b>To:</b><span class=apple-converted-space> </span><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:purple'>chimerax-users@cgl.ucsf.edu</span></a>; Wen-Jin Winston Wu <<a href="mailto:winston@gate.sinica.edu.tw"><span style='color:purple'>winston@gate.sinica.edu.tw</span></a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [chimerax-users] Open a PDB-formatted file and a MTZ file</span><span lang=EN-US><o:p></o:p></span></p></div></div></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Hi Winston,<span class=apple-converted-space> </span></span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>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.</span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Best regards,</span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Tristan</span><span lang=EN-US><o:p></o:p></span></p></div></div></div><div class=MsoNormal align=center style='text-align:center'><span lang=EN-US style='font-family:"Times New Roman",serif'><hr size=2 width="98%" align=center></span></div><div id=divRplyFwdMsg><div><div><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span class=apple-converted-space><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span></span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>ChimeraX-users <<a href="mailto:chimerax-users-bounces@cgl.ucsf.edu"><span style='color:#954F72'>chimerax-users-bounces@cgl.ucsf.edu</span></a>> on behalf of Wen-Jin Winston Wu via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:#954F72'>chimerax-users@cgl.ucsf.edu</span></a>><br><b>Sent:</b><span class=apple-converted-space> </span>22 June 2021 17:14<br><b>To:</b><span class=apple-converted-space> </span><a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:#954F72'>chimerax-users@cgl.ucsf.edu</span></a><span class=apple-converted-space> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu"><span style='color:#954F72'>chimerax-users@cgl.ucsf.edu</span></a>><br><b>Subject:</b><span class=apple-converted-space> </span>[chimerax-users] Open a PDB-formatted file and a MTZ file</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Times New Roman",serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div></div></div><div><div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>Hi,</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>I am trying to inspect electron density of X-ray data.</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>I have the PDB-formatted coordinate file a.pdb (not been submitted to PDB yet) and a mtz file (a.mtz).</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>I have downloaded Clipper to Chimera X (1.2.5) running on Window 10.<span class=apple-converted-space> </span></span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>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”.</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'>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!</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'><a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper"><span style='color:#954F72'>http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#clipper</span></a></span><span lang=EN-US><o:p></o:p></span></p></div></div><div><div><p class=MsoNormal><span lang=EN-US style='font-family:"Calibri",sans-serif'> </span><span lang=EN-US><o:p></o:p></span></p></div></div><p class=xmsonormal style='margin-bottom:12.0pt'><span lang=EN-US style='font-family:"Calibri",sans-serif'>Best wishes,<br><br>Winston</span><span lang=EN-US><o:p></o:p></span></p></div></div><div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>ChimeraX-users mailing list<br><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style='color:purple'>ChimeraX-users@cgl.ucsf.edu</span></a><br>Manage subscription:<br><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style='color:purple'>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></span><span lang=EN-US><o:p></o:p></span></p></div></div></blockquote></div><div><p class=MsoNormal><span lang=EN-US> <o:p></o:p></span></p></div></div><p class=MsoNormal><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>ChimeraX-users mailing list<br></span><span lang=EN-US><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>ChimeraX-users@cgl.ucsf.edu</span></a></span><span lang=EN-US style='font-size:9.0pt;font-family:"Helvetica",sans-serif'><br>Manage subscription:<br></span><span lang=EN-US><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"><span style='font-size:9.0pt;font-family:"Helvetica",sans-serif;color:purple'>https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p></o:p></span></p></div></blockquote></div><p class=MsoNormal><span lang=EN-US><o:p> </o:p></span></p></div></div></body></html>