<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 12, 2010, at 8:22 PM, Sumitro Harjanto wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-SG" link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Ok Eric, I think you can ignore my last email. I realised I can use “chimera –nogui –debug” to make the chimera command line appear and then I can open my .cmd file from there.</span></font></div></div></o:smarttagtype></div></span></blockquote><div><br></div>Yes, on Windows there really is no concept of "standard input" and "standard output" so in addition to --nogui you also have to supply --console (or --debug, which implies a console window) in order to see standard output and to supply standard input. We will try to make it so that --nogui with no script argument will also bring up a console window.</div><div><br></div><div>However, the point of my previous mail was that you don't need to type commands. If you just do this:</div><div><br></div><div>chimera --nogui myscript.py</div><div><br></div><div>Then Chimera will run "myscript.py" in nogui mode. You don't need to get a command prompt and type "open myscript.py".</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div lang="EN-SG" link="blue" vlink="blue" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"><div class="Section1"><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">But I realised also I cant save the reply log, which contain the rmsd information I need (my result!! T.T)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">I found this codet on the chimera mailing list:<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; ">def save_reply_log(path):<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> from chimera import dialogs<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> r = dialogs.find('reply')<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> text = r.text.get('1.0', 'end')<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> f = open(path, 'w')<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> f.write(text)<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "> f.close()<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 36pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; ">save_reply_log("/tmp/tmplog.txt")<o:p></o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0cm; margin-right: 0cm; margin-bottom: 0.0001pt; margin-left: 0cm; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span lang="EN" style="font-size: 10pt; font-family: Arial; color: navy; ">but how do I incorporate this into my .cmd..? or must I now script in python..?</span></font></div></div></o:smarttagtype></div></span></blockquote><div><br></div>There is no reply log in nogui mode. All the output will come to the console window. In order to copy from the console window you will need to right-click in the title bar of the console window.</div><div><br></div><div>--Eric<br></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>