pipeline:utilities:sxpdb2em

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pipeline:utilities:sxpdb2em [2018/08/22 11:05]
fmerino
pipeline:utilities:sxpdb2em [2019/04/02 09:33] (current)
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxpdb2em ​=====+===== sp_pdb2em ​=====
 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. 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.
  
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 Usage in command line Usage in command line
  
-  ​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+  ​sp_pdb2em.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
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxpdb2em ​does not support MPI.+sp_pdb2em ​does not support MPI.
  
-  ​sxpdb2em.py  tRNA.pdb ​ tRNA.hdf ​ --apix=2.26 ​ --box=150 ​ --center=c ​ --O  --quiet ​ --tr0=<'​filename'> ​ --het+  ​sp_pdb2em.py  tRNA.pdb ​ tRNA.hdf ​ --apix=2.26 ​ --box=150 ​ --center=c ​ --O  --quiet ​ --tr0=<'​filename'> ​ --het
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxpdb2em.py+sparx/bin/sp_pdb2em.py
  
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  • pipeline/utilities/sxpdb2em.txt
  • Last modified: 2019/04/02 09:33
  • by lusnig