chichaumiau / PED

PED: Point Electron Density

#PED: Point Electron Density

===============Install====================================================

1. Download chimera from https://www.cgl.ucsf.edu/chimera/ and install
   Find the binary execution of chimera in the 'bin' folder.
   
   
2. Replace the line 'chimera_bin=' in 'PED' file with your chimera dir
   

===============Usage======================================================
./PED pdb_file ccp4_file/omap_file
example: ./PED 1ehz.pdb 1ehz.ccp4

input files:

1. PDB file #standard PDB format, only 'ATOM' and 'HETATM' lines are considered
   
2. Electron density map file, ccp4 file/omap file, available at http://eds.bmc.uu.se/eds/
   Now the omap files are superseded by ccp4 files in PDBe: http://www.ebi.ac.uk/pdbe/eds.

output files:

1. '.dens' file, list of atoms with point electron density
   example:
   G A 1 OP3 99.85 1.16
   G A 1 P 100.19 1.88
   G A 1 OP1 100.19 0.95
   G A 1 OP2 99.21 1.18
   G A 1 O5' 99.82 1.54
   G A 1 C5' 98.63 0.92
   G A 1 C4' 97.84 1.03
   G A 1 O4' 97.10 0.93
   G A 1 C3' 98.07 1.08
   G A 1 O3' 99.39 1.05
   G A 1 C2' 96.96 1.53
   G A 1 O2' 96.77 0.99
   Residue=Ch===#Res======Atom===B factor=PointElecDensity
   
   
2. '.ent' file, PDB format file, the SegId column is replaced with point electron density
   example:
   ATOM 1 N GLN A 1 26.544 15.247 15.544 1.00 40.54 0.48 N
   ATOM 2 CA GLN A 1 27.006 15.744 16.843 1.00 23.59 2.12 C
   ATOM 3 C GLN A 1 25.837 16.192 17.710 1.00 19.71 2.69 C
   ATOM 4 O GLN A 1 25.930 17.211 18.394 1.00 20.35 3.41 O
   ATOM 5 CB GLN A 1 27.962 16.905 16.627 1.00 27.73 1.56 C
   ATOM 6 CG GLN A 1 27.432 17.948 15.648 1.00 48.19 1.02 C
   ATOM 7 CD GLN A 1 27.620 19.361 16.180 1.00 62.99 0.81 C
   ATOM 8 OE1 GLN A 1 28.461 19.615 17.051 1.00 52.44 0.80 O
   ATOM 9 NE2 GLN A 1 26.824 20.288 15.653 1.00 76.44 0.29 N
   =======================================================================segId==
   

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