Update README.md

README.md

@@ -1,14 +1,19 @@
 # subtomo2Chimera
 
+Convert Dynamo table, relion 4.0 star file to script to visualize in ChimeraX
+
 ## Required:
 [starfile](https://pypi.org/project/starfile/) and [eulerangles](https://pypi.org/project/eulerangles/) modules from Alister Burt
 
+If you use dynamotable2ChimeraX.py, you need to also install [dynamotable](https://pypi.org/project/dynamotable/)
+
 ```
 pip install eulerangles
 pip install starfile
+pip install dynamotable
 ```
 
-## Usage:
+## relionsubtomo2ChimeraX.py Usage:
 ```
 python relionsubtomo2ChimeraX.py --i run_data_empiar10064.star --o load_tomo1.cxc --avgAngpix 10.48 --avgBoxSize "64,64,64" --tomoname CTEM_tomo1
 ```
@@ -21,7 +26,35 @@ python relionsubtomo2ChimeraX.py --i run_data_empiar10064.star --o load_tomo1.cx
 
 *--avgBoxSize* Box Size of the average. 3 values seperated by comma and double quoted. Better be a cube. Not tested with non-cube yet.
 
-*--tomoname* Name of tomo for the visualization. You have to do this script for each tomo you want to visualize.
+*--tomoname* Name of tomo for the visualization. You have to do this script for each tomo you want to visualize. And the tomo name needs 100% match.
+
+Not required option
+
+*--avgFileName* Name of subtomo average loaded for the visualization. Default is *avg.mrc* but you can put any name in.
+
+*--offset* (default 0) Offset number if you want to load different kinds of subtomogram averages into the same session
+
+*--level* (default 0.0039) Volume level set for the subtomogram average
+
+
+## dynamotable2ChimeraX.py Usage:
+```
+python subtomo2Chimera/dynamotable2ChimeraX.py --tomoDoc tomograms.doc --i aligned.tbl --o load_tomo.cxc --avgAngpix 8.48 --tomoAngpix 8.48 --avgBoxSize "128,128,15" --tomoname CU428_TS013_rec.mrc
+```
+
+*--i* Input table file
+
+*--tomoDoc* Input tomo doc file
+
+*--o* Output ChimeraX Loading Script
+
+*--avgAngpix* Pixel Size of the average file
+
+*--avgBoxSize* Box Size of the average. 3 values seperated by comma and double quoted. Better be a cube. Not tested with non-cube yet.
+
+*--tomoname* Name of tomo for the visualization. You have to do this script for each tomo you want to visualize. Name needs 100% match
+
+*--tomoAngpix* Pixel size of the tomogram used for Dynamo table.
 
 Not required option
 
@@ -32,6 +65,8 @@ Not required option
 *--level* (default 0.0039) Volume level set for the subtomogram average
 
 
+
+
 ## How it works:
 The script will load the subtomogram average in Chimera and transform it to orientation of each subtomo in the tomogram. You can also load the tomogram in to visualize it together. This script only perform for only one kind of subtomogram average but it is not too difficult to do the same thing with different classes of average using the offset and combine the loading script together.
 
@@ -54,7 +89,7 @@ Script only works with relion 4.0 star file.
 The Chimera version of the script also works to a certain degree but it is very clumpsy and not properly aligned to the tomogram.
 
 ## How to run:
-1. Prepare the input files: Relion star file from Refine3D job (Should be at least 3.1 and up), the binned out subtomogram average avg.mrc (size ~1Mb)
+1. Prepare the input files: Relion star file from Refine3D job (Should be at least 3.1 and up), the binned out subtomogram average avg.mrc (size ~1Mb). For Dynamo, table & tomogram doc file, the binned out subtomogram average avg.mrc.
 
 2. Generate the ChimeraX loading script for a specific tomogram using the above command
 
@@ -64,6 +99,10 @@ Full command
 
 *python relionsubtomo2ChimeraX.py --i run_data_empiar10064.star --o load_tomo1.cxc --avgAngpix 10.48 --avgBoxSize "64,64,64" --tomoname CTEM_tomo1 --level 0.0039 --avgFileName avg.mrc --offset 0* 
 
+For dynamo command
+
+*python dynamotable2ChimeraX.py --tomoDoc tomograms.doc --i aligned.tbl --o load_tomo.cxc --avgAngpix 8.48 --tomoAngpix 8.48 --avgBoxSize "128,128,15" --tomoname CU428_TS013_rec.mrc
+
 3. Edit the ChimeraX loading script for proper level of the map and open the output script in Chimera using commandline or interface:
 
 *chimerax load_tomo1.cxc*