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QChASM / SEQCROW

Plug-in for ChimeraX providing features for building and manipulating organic and organometallic molecules as well as displaying output from quantum chemistry computations.
GNU General Public License v3.0
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`xTB` Error processing trigger "job finished" path should be string, bytes, ... #12

Closed MartinRJDagleish closed 11 months ago

MartinRJDagleish commented 11 months ago

Thank you very much for this superb extension for ChimeraX. I wanted to use the QM Input Generator for xTB, to optimize my 2D drawn input (I prefer xTB over AM1, PM6 or any other semi empirical calculation, because of speed and accuracy.)

Describe the bug When I use the QM Input Generator for xTB everything seems fine and the calculations also finish successfully, but the problem I have, is that the output does not get opened up again after the calculation finsihed.

Here I tried to put all windows together that are needed to reproduce. image

To Reproduce Steps to reproduce the behavior:

  1. Goto QM Inputer Generator
  2. Use xTB for given strucuture and use GFN2-xTB
  3. Set "open structure" for "when finished"
  4. After successful "job" get error

Additional context I am not sure if that is the problem, but when I look into the scratch folder I see that the folder containing my calculation has spaces in it of the form: "Phosphan_test_opt Fri Sep 29 12.44.08 2023" image

Could I be that the Python code does not support spaces in the path name for the folder? How can I change the folder name for the calculation?

ajs99778 commented 11 months ago

Thanks for reporting this. I appreciate the detailed pictures of what settings were used. The code can handle spaces, though it will replace spaces in the job name with underscores for orca jobs.

I think what's happening is seqcrow thinks there are multiple output .xyz files (this might be a bug - thinking there are multiple output file when there's only one). So, it makes a list of the .xyz files it finds. It should try to open each file in the list, but apparently there isn't code for that (definitely a bug). I'll look into this and do some more testing.

MartinRJDagleish commented 11 months ago

@ajs99778 Thank you very much for the fast response.

Please let me know if I can assist you in any way or if you need any more details. Otherwise I am hoping for a bugfix to fully utilize the extension to its full use.

ajs99778 commented 11 months ago

I've uploaded a patch to the tool shed that should fix this bug

MartinRJDagleish commented 11 months ago

@ajs99778 Thank you very much! Sry I was on holiday the last few days and could not respond sooner, but the change fixes everything for xTB now :)

Thanks for the quick fix!