[chimerax-users] How to open .py file downloaded from MOLEonline in ChimeraX?

[Kate Kim]

Thank you so much Elaine for such thorough and rapid instructions! I really
appreciate it!

When I tried opening a .py file in ChimeraX exported from Chimera, it gave
the following error and didn't work:

File
"/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Tunnels_only_4ChimeraX_wPDB.py",
line 41, in make_structure
from chimerax.pdb.pdb import set_logging_info
ImportError: cannot import name 'set_logging_info' from 'chimerax.pdb.pdb'
(/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/F0FF3182-52F0-41C1-88BD-EFCCE94E2CB5/d/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/pdb/pdb.py)

Error opening python file
/Users/katekim/Dropbox/Kate_private_pks13_ms/Pks13_ChimeraX_stuff/Tunnels_only_4ChimeraX_wPDB.py

However, the COLLADA option is good for me to use in this case as I'm only
trying to visualize the tunnels in ChimeraX.

Thank you,
Kate

On Sat, Oct 30, 2021 at 7:57 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Kate,
> Yes, the MOLEonline scripts are written just for Chimera. ChimeraX is a
> different program and won't work with Chimera sessions or python scripts
> written for Chimera.
>
> Chimera does have an option to export a file for input to ChimeraX, but it
> only includes the atomic/ribbon displays, not yet surfaces (but see below,
> to my surprise it worked!).  If the reason for using ChimeraX is display
> only (not calculations requiring atomic data), other Chimera export formats
> may also work, like Collada.  ChimeraX can read Collada files.
>
> See Chimera menu: File... Export Scene, options include ChimeraX and
> collada:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html>
> ... or Chimera's "export" command:
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>
>
> Just now I tested exporting a Chimera scene showing MOLEonline results
> (Chimera 1.16 daily build from August was what I had handy) and even though
> I got a warning message that the export to ChimeraX file does not work for
> surfaces, to my surprise, when I open it in ChimeraX, voila!  It does
> include the tunnel displays!  So maybe it WILL work for your situation. You
> may have to change the background color yourself.  I was also able to
> export collada (.dae) file from Chimera that gave the same display when
> opened in ChimeraX. The ChimeraX choice is better than collada, since it
> will also include all the other tunnels that aren't displayed when you
> export, see screenshot below:
>
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> How it looked in Chimera when I exported a file for ChimeraX
>
> How it looks in ChimeraX after I open that file (except I had to change
> background to white again myself), can hide/show all the tunnels.
>
>
> On Oct 29, 2021, at 7:37 PM, Kate Kim via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Hello,
> I've been using Chimera in the past for opening downloaded .py files from
> MOLEonline to visualize tunnels in my structure. When I try to do the same
> in ChimeraX, I get the following error:
>
> Traceback (most recent call last):
> File
> "/Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py",
> line 1, in <module>
> import chimera, _surface, numpy
> ModuleNotFoundError: No module named 'chimera'
>
> Error opening python
> file /Users/katekim/Downloads/mole_channels_6Qzq10eGEqLciv3DpeS8Q_1_chimera.py
> toolshed show
>
> Any suggestions on the best approach to visualize MOLE channels using
> ChimeraX?
>
> Thank you,
> Kate
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>
>
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