fixing logging typos and updating documentation

README.md

@@ -19,8 +19,9 @@ cryoDRGN installation, training and analysis. A brief quick start is provided be
 For any feedback, questions, or bugs, please file a Github issue or start a Github discussion.
 
 
-### New in Version 3.4.x
-* [NEW] `cryodrgn plot_classes` for analysis visualizations colored by a given set of class labels
+### Updates in Version 3.4.x
+* [NEW] `cryodrgn_utils plot_classes` for analysis visualizations colored by a given set of class labels
+* [NEW] `cryodrgn_utils make_movies` for animations of `analyze*` output volumes
 * implementing [automatic mixed-precision training](https://pytorch.org/docs/stable/amp.html)
   for ab-initio reconstruction for 2-4x speedup
 * support for RELION 3.1 .star files with separate optics tables, np.float16 number formats used in RELION .mrcs outputs
@@ -33,7 +34,7 @@ For any feedback, questions, or bugs, please file a Github issue or start a Gith
 * official support for Python 3.11
 
 
-### New in Version 3.x
+### Updates in Version 3.x
 
 The official release of [cryoDRGN-ET](https://www.biorxiv.org/content/10.1101/2023.08.18.553799v1) for heterogeneous subtomogram analysis.
 

cryodrgn/commands/abinit_het.py

@@ -901,7 +901,7 @@ def main(args):
             )
         if in_dim % 8 != 0:
             logger.warning(
-                f"Masked input image dimension {in_dim} is not a mutiple of 8 "
+                f"Masked input image dimension {in_dim} is not a multiple of 8 "
                 "-- AMP training speedup is not optimized!"
             )
 

cryodrgn/commands/train_vae.py

@@ -855,7 +855,7 @@ def main(args: argparse.Namespace) -> None:
             )
         if in_dim % 8 != 0:
             logger.warning(
-                f"Masked input image dimension {in_dim} is not a mutiple of 8 "
+                f"Masked input image dimension {in_dim} is not a multiple of 8 "
                 "-- AMP training speedup is not optimized!"
             )
 

cryodrgn/commands_utils/make_movies.py

@@ -1,4 +1,7 @@
-"""Make mp4 movies of .mrc's produced by analyze* commands
+"""Make MP4 movies of .mrc volumes produced by cryodrgn analyze* commands.
+
+You must install ChimeraX under the alias `chimerax` before running this command, see:
+https://www.cgl.ucsf.edu/chimerax/download.html
 
 Example usage
 -------------
@@ -9,7 +12,6 @@
 $ cryodrgn_utils make_movies spr_runs/07/out 19 volume --name=front --iso=210 --camera="0.12868,-0.9576,0.25778,95.4,-0.85972,-0.23728,-0.45231,15.356,0.4943,-0.16341,-0.8538,-33.755"
 
 """
-
 import argparse
 import os
 from datetime import datetime as dt