Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unit cell parameter is zero or negative #1033

Open
frgoe003 opened this issue Dec 15, 2024 · 0 comments
Open

Unit cell parameter is zero or negative #1033

frgoe003 opened this issue Dec 15, 2024 · 0 comments

Comments

@frgoe003
Copy link

Hello, I'm trying to run the reduce2 CLI with the flags approach=add, add_flip_movers=True, but for some systems I keep getting: ValueError: Unit cell parameter is zero or negative. Here are two examples of systems I am trying to process with reduce2: 8j3c, 4rsy

Here is the full traceback:

File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/mmtbx/command_line/reduce2.py", line 6, in <module> <br>
    run_program(reduce2.Program) <br>
  File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/iotbx/cli_parser.py", line 946, in run_program <br>
    task.run() <br>
  File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/mmtbx/programs/reduce2.py", line 1191, in run <br>
    self.model = shift_and_box_model(model=self.model, shift_model=False) <br>
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ <br>
  File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/cctbx/maptbx/box.py", line 1338, in shift_and_box_model <br>
    crystal_symmetry = crystal.symmetry((a, b, c, 90, 90, 90), 1) <br>
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ <br>
  File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/cctbx/crystal/__init__.py", line 70, in __init__ <br>
    unit_cell = uctbx.unit_cell(unit_cell) <br>
                ^^^^^^^^^^^^^^^^^^^^^^^^^^ <br>
  File "/home/fgoerlich/miniconda3/envs/docking/lib/python3.11/site-packages/cctbx/uctbx/__init__.py", line 46, in __init__ <br>
    ext.unit_cell.__init__(self, <br>
ValueError: Unit cell parameter is zero or negative.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant