Chimera-dev October 2017

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chimera-dev@cgl.ucsf.edu

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2 discussions

Chimera's default directory
by Shuto Araki 31 Oct '17

31 Oct '17

Hi everyone, My name is Shuto Araki, a Computer Science student at DePauw University in Indiana. I’m currently helping a research in biochemistry department using Chimera and Python. My program reads a csv file and manipulate and visualize its data on Chimera. I’m trying to read a csv file, but it only works on my computer because I have to use the absolute path for the csv file. Is there a way to set the path relative? How can I set the default directory to the one that I set in the Tool Preferences —> Locations? I tried os.getcwd() to see the default directory but the IDLE only returns “/“ and I’m confused because it is supposed to return a string representing the current working directory. Could you please help me figure out what’s happening? Sincerely, Shuto

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GUI question
by Daniel Gurnon 29 Oct '17

29 Oct '17

Hi everyone, I'm working with a undergraduate computer science student, Shuto Araki, on a Chimera development project that involves creating a GUI. I'm not a programmer, and he's learning Python as he goes- so we've run into the inevitable snag, and we're looking for some help. Here's how Shuto describes the issue: ---- I am trying to create a Chimera GUI extension that asks Chimera to fetch a PDB ID and then to highlight residue positions within the structure, with the PDB and positions taken from a CSV file. I started with a Python script, and it works as intended if I import it from IDLE. However, when I tried to create a GUI using this guide https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/ Examples/Main_ExtensionUI.html I ran into an error. When I click on the button that I added on toolbar, the callback function does not seem to work properly. It just pops up an empty window with OK, Apply and Cancel buttons. The code snippet is as follows: ############################################################## class MutationDialog(ModelessDialog): name = "mutation highlighter" title = "Rare Genetic Mutation Highlighter” master = Tk() master.title("Rare Genetic Disease Mutation Highlighter") master.geometry('{}x{}'.format(500, 100)) global var var = StringVar(master) var.set(proteinNames[0]) # proteinNames is a list of protein options that a user chooses options = OptionMenu(master, var, *proteinNames) options.pack() def Apply(): # this functionality works protein_num = proteinMap[var.get()] mh.highlightMutation(filename, protein_num) button = Button(master, text = "Apply", command = Apply) button.pack() chimera.dialogs.register(MutationDialog.name, MutationDialog) dir, file = os.path.split(__file__) icon = os.path.join(dir, 'ExtensionUI.tiff') chimera.tkgui.app.toolbar.add(icon, lambda d=chimera.dialogs.display, n=MutationDialog.name: d(n), 'Highlight Mutations', None) ############################################################## I suspect that MutationDialog class is not working as a proper callback class. *Do you have any suggestions for the proper structure of the class?* We're also Sincerely, Shuto --- Thanks for any advice! Dan ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry Director, Science Research Fellows Program DePauw University Greencastle, IN 46135

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