pdb2mrc

pdb2mrc is Eos's Command that converts from PDB file to mrcImage file by calculation of density.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-o	Optional	Output: mrcImage	NULL
-nx	Optional	Width x of Output image	1
-ny	Optional	Width y of Output image	1
-nz	Optional	Width z of Output image	1
-Sx	Optional	Reading start position x	0.0
-Sy	Optional	Reading start position y	0.0
-Sz	Optional	Reading start position z	0.0
-dx	Optional	Width of x per 1pixel	2.5
-dy	Optional	Width of y per 1pixel	2.5
-dz	Optional	Width of z per 1pixel	2.5
-w	Optional	Weight	1.0
-sig	Optional	Atom Radius: [A]	0.0
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0	Gaussian
1	WentzelAtomModel

Execution example

Input file's image

by pdbInfo

Input data

Use the options as the object falls within image.
In the case of this Input file, set the options as the following.

-nx	100
-ny	100
-nz	1
-Sx	-18
-Sy	-1
-Sz	0.5
-dx	0.5
-dy	0.5
-dz	60

Option -m

Case: m=0

Min Max Mean SD SE Sum

0 4 0.1364 0.39089 0.0039089 1364

Case: m=1

Min Max Mean SD SE Sum

0 9516.95 1100.45 1467.25 14.6725 1.10045e+07

Option -w

Case: w=10

image data before setting option


image data after setting option

Option -sig

Case: sig=1

Min Max Mean SD SE Sum

0 0.251258 0.0430626 0.0499095 0.000499095 430.626