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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Eric, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thank you for the quick response, and it was vey helpful, as the “window” command helped me find the structure (I’m not that familiar with Chimera, so thank for teaching me this command).
I was thinking the solution might have been placed somewhere far away from the map, but it turns out it was sent out to space, as the EM map and structure can been seen as two small dots after using the command. Anyway, that’s another problem.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Thank you!!
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Vilde<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> Eric Pettersen <pett@cgl.ucsf.edu>
<br>
<b>Sent:</b> onsdag 14. april 2021 22:35<br>
<b>To:</b> Vilde Leipart <vilde.leipart@nmbu.no><br>
<b>Cc:</b> Chimera <chimera-users@cgl.ucsf.edu><br>
<b>Subject:</b> ADP EM Chimera plugin<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal">Hi Vilde,<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Since ADP EM is a third-party plugin, I don't know that I know that much more than you about how it works. Hopefully the plugin developers
<i>will</i> get back to you. Nonetheless, I can offer some generic advice about seeing/finding the fitted structure. First, check the Model Panel (Favorites→Model Panel) to ensure that the structure model is shown (the "Shown" column for the structure model
is checked). Second, type the 'window' command (Favorites→Command Line) to ensure the view is large enough to show the position of the structure. Third, click on the color well in the Volume Viewer panel (the square next to "Color") and adjust the 'A' component
of the color (A = alpha, or opacity) so the the contour surface is semi-transparent, in case the structure is completely within a contour.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello, <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">I’m trying to use the ADP EM molecular fitting tool (Chimera Plugin) to fit my PDB-models into a low resolution map. The plugin works as it should, but I’m having trouble visualizing the solutions. Once the fitting is
finished (the table with all the coordinates is produced) and I chose for example solution 1, the PDB structure disappears in the Chimera Window. The EM map is still showing. If I click on the “Back to initial”-button, the PDB structure comes back, but in
the initial position, of course. I have tried to save the solutions, but they are still not showing (the solutions are selected as “show” as a cartoon in the model panel). According to the description of the plugin developers, the solutions/fits should be
visualized just by selecting one, no extra steps needed. </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">I’m doing something wrong in Chimera or is there a bug?</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far.</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US">Best regards, </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:#222222">Vilde Leipart</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:12.0pt;color:#222222">PhD-student,</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#222222">Faculty of Environmental Sciences and Natural Resource Management,</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222"> </span><span lang="EN-US" style="font-size:10.0pt;color:#222222">Norwegian
University of Life Sciences</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#222222">Høgskoleveien 12, 1430 Ås, Norway</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#222222"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#222222">Honey Bee Research Lab, Arizona Sate University</span><o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;color:#222222">427 East Tyler Mall, Tempe, AZ 85287</span><o:p></o:p></p>
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