[chimerax-users] Color electrostatic ValueError

[Maria Maldonado]

Elaine and Tom,

Thank you very much for your help, I'll try the newer version. Apologies, I didn't know about the bug report procedure and wasn't sure this was a bug __ I'll use the Help/report bug from now on.

Best,
Maria



On 7/14/20, 4:37 PM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:

    Hi Maria,
    I used this exact command on structure 2gbp and 2gbp.cube that I got from the Delphi server in December 2019, and it worked fine in all three versions of ChimeraX that I tested: 0.91 (the old version you are using), 1.0 (most recent production release), and July 9 daily build. 

    We recommend you get a newer version, but at least my tests suggest it may not matter for this specific issue.

    All I can say is that there could be some problem with the specific cube file, and/or it is possible that the Delphi server changed between when I saved my cube file and when you saved yours.

    It's fine to ask questions on this list, but for bug reports specifically, it is best not to send it to this list.  Instead, when you get the error, immediately use the bug reporter dialog (the error dialog may have a button to report bug, or if not, you can use menu: Help... Report a Bug).  This will automatically include log contents and information about version.  You should also attach any data needed to reproduce the problem, such as your cube file if you don't mind sharing it, and include your e-mail address if you want feedback about your report.

    I hope this helps,
    Elaine
    -----
    Elaine C. Meng, Ph.D.                       
    UCSF Chimera(X) team
    Department of Pharmaceutical Chemistry
    University of California, San Francisco

    > On Jul 14, 2020, at 4:19 PM, Maria Maldonado <mmaldo at ucdavis.edu> wrote:
    > 
    > Hello ChimeraX team,
    >  
    > I was hoping you could help me with a python error I get when trying to use the color electrostatic command.
    >  
    > I have my protein surface and my electrostatic map from Delphi in cube format. When I run “color electrostatic #1 map #2  palette -10,red:0,white:10,blue”, I get long error ending in “ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
    >  
    > File "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/gaussian/gaussian_format.py", line 120, in matrix
    > if self.matrices == None:
    > 
    > See log for complete Python traceback.” (I can send you the full error if useful.)
    >  
    > I don’t get the error if I use a Delphi .phi file. However, the .phi files from this Delphi version have a bug that distorts the map, so the Delphi developers recommended using the .cube format instead. (The newer version of Delphi does not seem available for Mac at the moment.)
    >  
    > Is the ValueError to do with ChimeraX or is it something to do with the .cube files? Do you have any suggestions as to how to solve this?
    >  
    > Thank you very much for all your help,
    > Maria