mrcImagepdbFileReduce

From EosPedia
Jump to: navigation, search

mrcImagepdbFileReduce is Eos's Command that subtracts expected density from PDB.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage NULL
-p Essential Input: PDB NULL
-o Essential Output: mrcImage NULL
-t Essential Threshold 0
-r Optional Radius of Atom 1
-v Optional [PDB]] file's PixelVaule 0
-IT Optional Threshold for interface recognition 0
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help  


-m details

Value Description
0


Execution example

Input file's image

-i file's image

Input-1B7T.png
xy-plane

Input1-1B7T.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

21001.7 (30, 26, 27)
213.171
1416

2.67599


-p file's Image
Input-1VOM-PDB.png

Gravity Centre(CA)

Atom far from Centre(CA)

Atom far from Centre(CA, Axis)

6.727136e+01 3.631518e+01 -2.983928e+01

5.314867e+01

40.92 41.49 48.47


Case: Options only essential

Case: t=10000

Outdata-mrcImagepdbFileReduce.png
xy-plane

Outdata1-mrcImagepdbFileReduce.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

21001.7 (30, 26, 27)
102.239
1187.54

2.24424


In the following, Setting att=10000

Option -r

Case: r=70

Case: No other settings
Output
3A 
4A 
5A 
6A 
7A 
8A 
9A 
10A 
11A 
12A 

...

1691A 
1693A 
1695A 
1696A 
1697A 
1698A 
1699A 
1700A 
1703A 
1704A 


-o 's image

Outdata-r-mrcImagepdbFileReduce.png
xy-plane

Outdata1-r-mrcImagepdbFileReduce.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

20982.9 (33, 29, 34)
72.6667
1003.8

1.897


Case: ITh=20000
Output
6A 
7A 
8A 
9A 
10A 
14A 
20A 
22A 
23A 
24A 
1231A 
1242A 
1344A 
1360A 
1361A 
1540A 
1553A 
1616A 
1663A 


-o 's image

Outdata-ITh-mrcImagepdbFileReduce.png
xy-plane

Outdata1-ITh-mrcImagepdbFileReduce.png
yz-plane

Min

Max
Mean
SD

SE

0 (0, 0, 0)

20982.9 (33, 29, 34)
72.6667
1003.8

1.897


Option -v

Case: v=10000

Outdata-v-mrcImagepdbFileReduce.png
xy-plane

Outdata1-v-mrcImagepdbFileReduce.png
yz-plane

Min

Max
Mean
SD

SE

10000 (0, 0, 0)

21001.7 (30, 26, 27)
10026.6
362.839

0.685702