Differences

This shows you the differences between two versions of the page.

--- pipeline:utilities:sxpdb2em [2018/05/14 16:19]
127.0.0.1 external edit
+++ pipeline:utilities:sxpdb2em [2018/08/22 11:05]
fmerino
@@ Line 2: / Line 2: @@
 ===== sxpdb2em =====
-PDB File Conversion: Converts an atomic model into a simulated density map.
+PDB File Conversion: Converts an atomic model stored in a PDB file into a simulated electron density map. The coordinates (0,0,0) in PDB space will map to the center of the volume.
 \\
@@ Line 9: / Line 9: @@
 Usage in command line
-  sxpdb2em.py  input_pdb  output_hdf  --apix=pixel_size  --box=box_size  --het  --center=center  --O  --tr0=matrix_file  --quiet
+  sxpdb2em.py  input_pdb  output_hdf  --apix=PIXEL_SIZE  --box=BOX_SIZE  --het  --chains=CHAIN_STRING --center=CENTERING_METHOD  --O  --tr0=MATRIX_FILE_PATH  --set_apix_value=PIXEL_SIZE_STRING  --quiet
 \\
@@ Line 25: / Line 25: @@
   ; %%--%%apix : Pixel size of output map [A]: Pixel size of the output map [A]. (default 1.0)
-  ; %%--%%box : Output box size [Voxels]: If not given, the program will find the minimum box size fitting the structure. Be aware that this will most likely result in a rectangular box. (default required int)
+  ; %%--%%box : Output box size [Voxels]: Specify string of a single value (e.g. '256') to get a cubic box. Alternatively, use 'x,y,z' format to specify demensions of x,y,z-axis (e.g. '128,64,256'). If not given, the program will find the minimum box size fitting the structure. Be aware that this will most likely result in a rectangular box. Note that GUI does not support the default mode. (default required string)
   ; %%--%%het : Include hetero atoms: Otherwise, the HETATM entries in the PDB file are ignored. (default False)
-  ; %%--%%center : Center model at the origin: Specifies whether the atomic model should be moved to the origin before generating density map. Available options are: c - Use the geometrical center of atoms; a - Use the center of mass (recommended); x,y,z - Vector to be subtracted for the coordinates. Default: no centering, in which case (0,0,0) in the PDB space will map to the center of the EM volume. (default n)
+  ; %%--%%chains : Chain identifiers: A string list of chain identifiers to include (e.g. 'ABEFG'). By default, all chains will be included. (default none)
-  ; %%--%%O : Apply additional rotation: This can be used to modify the orientation of the atomic model. (default False)
+  ; %%--%%center : Center model at the origin: Specifies whether the atomic model should be moved to the origin before generating density map. Available options are: 'c' - Use the geometrical center of atoms; 'a' - Use the center of mass (recommended); 'x,y,z' - Vector to be subtracted from all PDB coordinates. 'n' - No centering, in which case (0,0,0) in the PDB space will map to the center of the EM volume. (default n)
+  ; %%--%%O : Apply additional rotation: This can be used to modify the orientation of the atomic model by using O system of coordinates. (default False)
   ; %%--%%tr0 : Rotational matrix file: This file must contain the 3x4 transformation matrix to be applied to the PDB coordinates after centering. The translation vector (last column of the matrix) must be specified in Angstrom. (default none)
+  ; %%--%%set_apix_value : Set header pixel size: Set pixel size in header of the ouput map. (default False)
 \\
 === Advanced Parameters ===
-  ; %%--%%quiet : Silent mode: Does not print any information to the monitor. (default False)
+  ; %%--%%quiet : Silent mode: Does not print any information to the monitor. Verbose is the default. (default False)
 \\
@@ Line 75: / Line 77: @@
 \\

User Tools

Site Tools

Differences

Page Tools