pdbNearAtomListShow

pdbNearAtomListShow is Eos's Command that shows near atom information.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-o	Optional	Output: ASCII(Coordinates List)	stdout
-P	Optional	POI: (Px, Py, Pz)	(0.0, 0.0, 0.0)
-V	Optional	VOI: mrcImage	NULL
-C	Optional	ContourLevel for VolumeOfInterest(For -V only)	0.0
-d	Optional	Distance: [A]	0.0
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

Select either -P or -V. (-P takes priority.)

-m details

Value	Description
0

Execution example

Input file image

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

6.053012e+00 2.519590e+01 1.189075e+01 3.286664e+01 24.77 23.85 28.04

Case: Options only essential

No ATOM

On this input file and default setting, it can't find atoms.

Option -P, -d

Case: P=(25, 25, 25), d=4

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

2.462900e+01 2.550600e+01 2.299300e+01 5.227511e+00 2.81 2.28 5.20

Option -V

-V file's image

xy-plane

yz-plane

Min Max Mean SD SE

0 (0, 0, 0) 3500.79 (24, 28, 5) 88.3104 323.414 0.914753

Case: d=0.3

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

4.250222e+00 2.688167e+01 1.551100e+01 2.727775e+01 21.57 22.63 26.38

Case: C=3500, d=0.3

Gravity Centre(CA) Atom far from Centre(CA) Atom far from Centre(CA, Axis)

5.977000e+00 2.695800e+01 -1.009600e+01 0.000000e+00 0.00 0.00 0.00