jaimergp
commented
5 years ago You should have obtained a warning about the NumPy version during the installation (check here for the relevant code).
In short, you must update Chimera's Numpy with:
conda activate ~/tangram
pip install -U 'numpy==1.11.*' -t $(pychimera --path)/lib/python2.7/site-packagesTake into account that this operation cannot be undone, and some extensions in Chimera will stop working (those depending on MMTK, mainly, but also any other relying on the deprecated numpy.numeric). If you need those, you can always install a new Chimera instance in a different directory.
JeanDidier
Hello,
I have the following problem with the calculation of the normal modes. When trying to open on linux the normal mode interface I have:
RuntimeError: module compiled against API version 0xa but this version of numpy is 0x7 /home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/scipy/init.py:115: UserWarning: Numpy 1.8.2 or above is recommended for this version of scipy (detected version 1.7.2) UserWarning) RuntimeError: module compiled against API version 9 but this version of numpy is 7 RuntimeError: module compiled against API version 9 but this version of numpy is 7 ImportError Exception in Tk callback Function: <function activate at 0x7f7298c276e0> (type: <type 'function'>) Module: <module 'chimera.extension.base' from '/home/jeandi/.local/UCSF-Chimera64-1.13.1rc/share/chimera/extension/base.pyc'> (line: 487) Args: () Traceback (innermost last): File "/home/jeandi/.local/UCSF-Chimera64-1.13.1rc/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py", line 1747, in call return apply(self.func, args) File "/home/jeandi/.local/UCSF-Chimera64-1.13.1rc/share/chimera/extension/base.py", line 488, in activate e.menuActivate(cat) File "/home/jeandi/.local/UCSF-Chimera64-1.13.1rc/share/chimera/extension/base.py", line 91, in menuActivate self.activate() File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/normalmodes/ChimeraExtension.py", line 23, in activate self.module('gui').showUI() File "/home/jeandi/.local/UCSF-Chimera64-1.13.1rc/share/chimera/extension/base.py", line 113, in module mod = import(fullName) File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/normalmodes/gui.py", line 12, in
from core import Controller
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/normalmodes/core.py", line 11, in
import prody
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/prody/init.py", line 95, in
from . import dynamics
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/prody/dynamics/init.py", line 242, in
from . import rtb
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/prody/dynamics/rtb.py", line 12, in
from scipy import sparse
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/scipy/sparse/init.py", line 231, in
from .csr import *
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/scipy/sparse/csr.py", line 15, in
from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
ImportError: numpy.core.multiarray failed to import
ImportError: numpy.core.multiarray failed to import
File "/home/jeandi/miniconda3/envs/tangram/lib/python2.7/site-packages/scipy/sparse/csr.py", line 15, in
from ._sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \
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