mrcImage2pdb

mrcImage2pdb is Eos's Command that converts mrcImage file to PDB file. Output PDB file consists of all alpha carbon.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage	NULL
-o	Essential	Output: PDB	NULL
-hi	Optional	Value of high threshold. Default is the MAX.	0
-lo	Optional	Value of low threshold. Default is the MIN.(Only m=0, 1)	0
-L	Optional	Atoms are on lattice points. (Only m=2 - 4)
-Skip	Optional	Skip atoms.	1
-R	Optional	Random	0
-d	Optional	Delta to select atoms to avoid too much concentration. (Range: 0 - 0.5) (Only m=2 - 4)	0.1
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	5
-h	Optional	Help

-m details

Value	Description
0	One atom for one boxel.
1	Eight atoms for one boxel.
2	On the surface of high threshold. Atoms few.
3	On the surface of high threshold. Atoms medium.
4	On the surface of high threshold. Atoms many
5	(Default) : On the surface of high threshold. Mesh mode.

Execution example

Input file image

xy-plane

yz-plane

Min Max Mean SD SE

0 (0, 0, 0) 4.07334 (34, 9, 75) 0.00164516 0.0572113 8.29149e-05

Option -hi

Case: hi=1e-3

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

2.708889e+02 2.744812e+02 3.518376e+02 3.279044e+02 205.11 206.48 252.16

Option -Skip

Case: Skip=10, hi=1e-3

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

2.617321e+02 2.673613e+02 3.468850e+02 3.360901e+02 214.27 208.64 253.12

Option -R

Case: R=10, hi=1e-3

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

2.707916e+02 2.743434e+02 3.520507e+02 3.468584e+02 225.08 226.31 271.93

Option -m

Case: m=0

Case: No other settings

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

2.703961e+02 2.755795e+02 3.510611e+02 3.218664e+02 201.60 203.58 248.94

Case: lo=2

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

2.782154e+02 2.705846e+02 3.485538e+02 3.201251e+02 206.22 201.42 251.45

Case: m=1

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

2.703961e+02 2.755795e+02 3.510611e+02 3.251428e+02 203.60 205.58 250.94

Case: m=2, hi=1e-3

Case: No other settings

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

2.705893e+02 2.743574e+02 3.518459e+02 3.277470e+02 209.41 210.36 256.15

Option -L

Blue: With -L Brown: Without -L

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

2.706073e+02 2.744103e+02 3.517186e+02 3.247068e+02 205.39 206.41 252.28

Case: d=1e-3

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

2.704110e+02 2.745547e+02 3.517133e+02 3.278861e+02 209.59 210.55 256.28

Case: m=3, hi=1e-3

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

2.706223e+02 2.741782e+02 3.517764e+02 3.322329e+02 209.37 210.18 256.22

Case: m=4, hi=1e-3

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

2.707323e+02 2.740721e+02 3.517465e+02 3.347665e+02 209.26 210.07 256.25