Tom Goddard
Tom Goddard
I added a two lower level routines to plot a single colored protein backbone using matplotlib and plot a single PAE heatmap. These new routines are in colabfold.py and are...
I updated from PyOpenVR 1.3.2201 to 1.5.1701 and openvr.init(openvr.VRApplication_Scene) fails with 'VRInitError_Init_InterfaceNotFound' (error number 105) It fails in 1.5.1701 but not in 1.3.2201. In PyOpenVR.__init__.py version 1.5.1701 has IVRSystem_Version =...
The error message when pyopenvr fails to connect to SteamVR because an API version is not available should be more informative. Currently it says VRInitError_Init_InterfaceNotFound (error number 105) With this...
The initialization error code 1002 is not listed in pyopenvr/error_codes/__init__.py and this causes a cryptic KeyError instead of reporting why initialization failed. It looks like this error code is “Oculus...
In AlphaFold 2.2.4 the pickled per-structure output files from a multimer prediction such as result_model_1_multimer_v2_pred_0.pkl now contains a JAX dependency (apparently a jax DeviceArray structure was pickled). This prevents the...
Do you plan to update ColabFold to use AlphaFold 2.3.0? It uses less memory running multimer predictions allowing larger structure predictions that would be very valuable for researchers. Here are...
The current ColabFold with OpenMM updated from 7.5.1 to 7.7.0 does not have a git version tag. The most recent ColabFold version tag v1.5.2 from March 4, 2023 has the...
The PAE plots produced by colabfold.py plot_pae() are missing the horizontal and vertical black divider lines between chains when the axes argument is specified (it is specified by ChimeraX). The...
There is a bug in the setup_logging() routine in colabfold/colabfold/utils.py. If setup_logging() is called twice for two consecutive runs in a Python notebook then no log messages appear. ChimeraX was...
I'm making a cryoDRGN visualization tool in ChimeraX and am interested in any suggestions users have about what it should do. So far it shows the umap plot and the...