[Chimera-users] ADP EM Chimera plugin

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 15 09:08:54 PDT 2021

Happy to help!


> On Apr 15, 2021, at 12:36 AM, Vilde Leipart <vilde.leipart at nmbu.no> wrote:
> Hi Eric, 
> 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.
> Thank you!!
> Vilde
> From: Eric Pettersen <pett at cgl.ucsf.edu> 
> Sent: onsdag 14. april 2021 22:35
> To: Vilde Leipart <vilde.leipart at nmbu.no>
> Cc: Chimera <chimera-users at cgl.ucsf.edu>
> Subject: ADP EM Chimera plugin
> Hi Vilde,
>               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 will 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.
> --Eric
>               Eric Pettersen
>               UCSF Computer Graphics Lab
> Hello, 
> 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. 
> I’m doing something wrong in Chimera or is there a bug?
> I have tried with the two latest versions of Chimera for Windows (1.14 and 1.15), with the same result.
> Any help or advice would be much appreciated! I have also tried to contact the developers of the plugin, but no response so far.
> Best regards, 
> Vilde Leipart
> PhD-student,
> Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences
> Høgskoleveien 12, 1430 Ås, Norway
> Honey Bee Research Lab, Arizona Sate University
> 427 East Tyler Mall, Tempe, AZ 85287
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