<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div></div><div><br><div><div>On Aug 20, 2008, at 9:37 AM, James A. Cleland 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: 16px; 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: 0; "><div lang="EN-US" link="blue" vlink="purple" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Ok, I ran this in chimera (gui) and I see how it is working now, the reply contains space-separated coordinates at the end of the string and get_coords picks these off from the end (-1, -2, -3). Perhaps this is another “headless” issue as there is no dialog? If so, maybe there’s somewhere else I can pick off the reply information for getcrd?<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Thanks!<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: 0in; "><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>James A. Cleland [<a href="mailto:jcleland@jamescleland.com" style="color: blue; text-decoration: underline; ">mailto:jcleland@jamescleland.com</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, August 20, 2008 12:32 PM<br><b>To:</b><span class="Apple-converted-space"> </span>'Eric Pettersen'<br><b>Subject:</b><span class="Apple-converted-space"> </span>RE: headless chimera issues<o:p></o:p></span></div></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">This worked like a charm, thank you! I have run into another issue that I thought you may be able to help with.<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">We are attempting to draw a pointer indicating the alpha carbon for a particular residue. This has been done in the past, but no longer works. This may have been something that you helped with.<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">The function that is currently failing is called “get_coords()”. Here’s what I have:<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; ">def</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span><b>_get_coords</b>():</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> <span class="Apple-converted-space"> </span></span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; ">from</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span>chimera<span class="Apple-converted-space"> </span></span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; ">import</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span>dialogs, Vector</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coords = Vector(</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">0</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">,</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">0</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">,</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">0</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">)</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> r = dialogs.find(</span><i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: rgb(0, 170, 0); ">'reply'</span></i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">)</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> text = r.text.get(</span><i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: rgb(0, 170, 0); ">'1.0'</span></i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">,<span class="Apple-converted-space"> </span></span><i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: rgb(0, 170, 0); ">'end'</span></i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">)</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coordString = text.splitlines()[-</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">2</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">]</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coordString = coordString.split(</span><i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: rgb(0, 170, 0); ">' '</span></i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">)</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> <span class="Apple-converted-space"> </span></span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; ">print</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span>coordString</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coords[</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">2</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">] = float(coordString[-</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">1</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">])</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coords[</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">1</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">] = float(coordString[-</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">2</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">])</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> coords[</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">0</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">] = float(coordString[-</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: maroon; ">3</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; ">])</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> <span class="Apple-converted-space"> </span></span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: blue; ">return</span><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span>cords<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Prior to calling get_coords(), there is a command executed that seems to provide the dialog information, if I’m understanding correctly:<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "> runCommand(</span><i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: rgb(0, 170, 0); ">"getcrd #0:%s.%s@CA"</span></i><span style="font-size: 8pt; font-family: 'Lucida Console'; color: black; "><span class="Apple-converted-space"> </span>% (snpPos, chain))</span><span style="font-size: 8pt; font-family: 'Lucida Console'; "><o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">The line that appears to be failing in get_coords() is the fourth in the function, r.text.get(). It looks like dialogs.find() returned None.<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Do you have any suggestions as to how I might get these coordinates or what we might be doing wrong?<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Thanks!<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">James<o:p></o:p></span></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; border-top-color: rgb(181, 196, 223); border-top-width: 1pt; padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: 0in; "><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; ">From:</span></b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; "><span class="Apple-converted-space"> </span>Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">mailto:pett@cgl.ucsf.edu</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Tuesday, August 19, 2008 7:41 PM<br><b>To:</b><span class="Apple-converted-space"> </span>James A. Cleland<br><b>Cc:</b><span class="Apple-converted-space"> </span>Tom Goddard<br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: headless chimera issues<o:p></o:p></span></div></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">That's right -- the patch just prevents the error. It doesn't do the coloring. Hopefully Tom Goddard will be able to help you with that.<o:p></o:p></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">--Eric<o:p></o:p></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; ">On Aug 19, 2008, at 4:21 PM, James A. Cleland wrote:<o:p></o:p></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div><div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Thank you for the quick reply! I applied this patch manually by just adding the import and the condition. I had commented the conditional statements prior to writing you and this worked fine, but the surface model didn’t appear to be colored according to the Delphi output. Is it correct for me to assume that, after this patch is applied, I’m still not seeing the electrostatic potential in the surface coloring?</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "> </span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">Thanks again,</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); ">James</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: rgb(192, 80, 77); "> </span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="border-right-style: none; border-bottom-style: none; border-left-style: none; border-width: initial; border-color: initial; border-top-style: solid; padding-top: 3pt; padding-right: 0in; padding-bottom: 0in; padding-left: 0in; border-width: initial; border-color: initial; "><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">From:</span></b><span class="apple-converted-space"><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; "> </span></span><span style="font-size: 10pt; font-family: Tahoma, sans-serif; color: black; ">Eric Pettersen [<a href="mailto:pett@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">mailto:pett@cgl.ucsf.edu</a>]<span class="apple-converted-space"> </span><br><b>Sent:</b><span class="apple-converted-space"> </span>Tuesday, August 19, 2008 6:56 PM<br><b>To:</b><span class="apple-converted-space"> </span>James A. Cleland<br><b>Cc:</b><span class="apple-converted-space"> </span>Tom Goddard<br><b>Subject:</b><span class="apple-converted-space"> </span>Re: headless chimera issues</span><span style="color: black; "><o:p></o:p></span></div></div></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">Hi James,<o:p></o:p></span></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-tab-span"><span style="color: black; "> </span></span><span class="apple-converted-space"><span style="color: black; "> </span></span><span style="color: black; ">That exception would be a bug -- SurfaceColor should not be trying to bring up a dialog if Chimera is running in nogui mode. I've committed a fix for this and it will be in tomorrow's daily build. Here's the diff if you want to correct your version:<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div></div><div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">*** ChimeraExtension.py<span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>6 May 2008 04:20:05 -0000<span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>1.12<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">--- ChimeraExtension.py<span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>19 Aug 2008 22:51:36 -0000<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">***************<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">*** 50,56 ****<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> from VolumeViewer import open_volume_file<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> vlist = open_volume_file(path, ftype, open_models = False,<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span> show_data = False, show_dialog = False)<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">! if len(vlist) > 0:<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> from SurfaceColor.gui import show_surface_color_dialog<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>d = show_surface_color_dialog()<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>d.use_electrostatics_colormap()<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">--- 50,57 ----<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> from VolumeViewer import open_volume_file<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> vlist = open_volume_file(path, ftype, open_models = False,<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span> show_data = False, show_dialog = False)<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">! import chimera<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">! if len(vlist) > 0 and not chimera.nogui:<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> from SurfaceColor.gui import show_surface_color_dialog<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>d = show_surface_color_dialog()<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <span class="apple-tab-span"> </span><span class="apple-converted-space"> </span>d.use_electrostatics_colormap()<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-tab-span"><span style="color: black; "> </span></span><span class="apple-converted-space"><span style="color: black; "> </span></span><span style="color: black; ">I've cc'ed Tom Goddard on this mail since he is the expert on Chimera's volumetric API and can hopefully provide advice on coloring your map programmatically.<o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">--Eric<o:p></o:p></span></div></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-converted-space"><span style="font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-family: Helvetica, sans-serif; color: black; ">Eric Pettersen</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-converted-space"><span style="font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-family: Helvetica, sans-serif; color: black; ">UCSF Computer Graphics Lab</span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span class="apple-converted-space"><span style="font-family: Helvetica, sans-serif; color: black; "> </span></span><span style="font-family: Helvetica, sans-serif; color: black; "><a href="http://www.cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">http://www.cgl.ucsf.edu</a></span><span style="color: black; "><o:p></o:p></span></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-family: Helvetica, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div><div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; ">On Aug 19, 2008, at 1:32 PM, James A. Cleland wrote:<o:p></o:p></span></div></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "><br><br><o:p></o:p></span></div></div><div><div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">Hi Eric,</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">My name is James Cleland and I am currently working with Dr. Rachel Karchin at JHU. I had corresponded with Greg Couch over running Chimera without an X server and he had directed me toward a build designed to run headless. I have been using this for a couple of weeks without problems, but I encountered an issue the other day.</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">I am trying to import a surface for electrostatic potential that was generated using Delphi. The trouble is, this is causing an error (see below).</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">Executing test.py...Opening pdb1a01.ent...</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">1 model opened</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">Traceback (most recent call last):</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "/home/pipeline/chimera/share/__main__.py", line 65, in <module></span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> value = chimeraInit.init(sys.argv)</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimeraInit.py", line 384, in init</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> chimera.openModels.open(a, prefixableType=1)</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/__init__.py", line 1345, in open</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "test.py", line 15, in <module></span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> runCommand("open 1a01.phi")</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/__init__.py", line 2026, in runCommand</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/Midas/midas_text.py", line 918, in doOpen</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "<string>", line 1, in <module></span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/Midas/__init__.py", line 1352, in open</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/__init__.py", line 1345, in open</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/SurfaceColor/ChimeraExtension.py", line 55, in open_cb</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/SurfaceColor/gui.py", line 613, in show_surface_color_dialog</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/dialogs.py", line 77, in display</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/dialogs.py", line 62, in find</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/baseDialog.py", line 435, in __init__</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/baseDialog.py", line 121, in __init__</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> File "CHIMERA/share/chimera/tkgui.py", line 63, in <module></span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">ImportError: No module named Togl</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">Error while processing test.py:</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">ImportError: No module named Togl</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">(see reply log for Python traceback info)</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">From what I can gather, the call to open is trying to present a dialog for choosing surface colors and limits. I’ve seen this when running Chimera with an X server. The trouble is, I need to skip this dialog and, possibly, specify volume in some other fashion.</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">We used to use the following python code in our Chimera script:</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">from chimera import openModels, MSMSModel</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">runCommand("set bg_color black")</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">surf = openModels.list(modelTypes=[MSMSModel])[0]</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">from VolumeViewer.volume import Volume</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">vol = openModels.list(modelTypes=[Volume])[0]</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">from SurfaceColor import color_by_volume</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); ">color_by_volume(surf, vol, (-30, 0, 30), ((1,0,0,1.0), (1,1,1,1.0), (0,0,1,1.0)))</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 8pt; font-family: 'Courier New'; color: rgb(166, 166, 166); "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">This was run using an older version of Chimera and used an X server. We ran into problems using this version with –nogui, which is what led me to the headless version.</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-family: Calibri, sans-serif; color: black; ">I have been playing around with SurfaceColor/ChimeraExtensions.py, specifically line 55-56, trying to figure out how to at least get color on the surface using the default volume. It appears that, by commenting the aforementioned lines, I get no surface coloring at all.</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">Can you provide some direction for me on this? Any help is appreciated!</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; ">Thanks,</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11.5pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(79, 129, 189); ">James A. Cleland</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(79, 129, 189); ">(w) 1(703)392-1357</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(79, 129, 189); ">(c) 1(703)402-5447</span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(79, 129, 189); "><a href="mailto:jcleland@jamescleland.com" style="color: blue; text-decoration: underline; ">jcleland@jamescleland.com</a></span><span style="color: black; "><o:p></o:p></span></div></div></div><div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; "> </span><span style="color: black; "><o:p></o:p></span></div></div></div></div></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="color: black; "> <o:p></o:p></span></div></div></div></div></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif; "><o:p> </o:p></div></div></div></div></span></blockquote></div><br></div></body></html>