Difference between revisions of "pdbAtomSection"

Revision as of 06:10, 7 August 2014 (view source) Kinoshita (Talk | contribs) (→‎Main option) ← Older edit		Latest revision as of 06:35, 7 August 2014 (view source) Kinoshita (Talk | contribs) (→‎Main option)
Line 20:		Line 20:
	<td>-if</td>		<td>-if</td>
	<td>Optional</td>		<td>Optional</td>
−	<td>Input: FlagsFile</td>	+	<td>Input: [[ASCII]](FlagsFile)</td>
	<td>NULL</td>		<td>NULL</td>
	</tr>		</tr>

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Latest revision as of 06:35, 7 August 2014

pdbAtomSection is Eos's Command that cuts out section from Atoms Model, and outputs to ps file.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-if	Optional	Input: ASCII(FlagsFile)	NULL
-o	Essential	Output: psfile	NULL
-dist	Optional	Distance of Sections	2.5
-zmin	Optional	z min	0.0
-zmax	Optional	z max	90.0
-fm	Optional	flag mode	13
-r	Optional	radius	1.0
-clw	Optional	Width of Circle	0.1
-plw	Optional	Width of Peptide bond	0.1
-fontsize	Optional	font size	2.0
-AS	Optional	absolute scale of PS file (-AS 1 := 1 mm/A)	1.0
-shiftx	Optional	pdb Shift x [A]	0.0
-shifty	Optional	pdb Shift y [A]	0.0
-shiftz	Optional	pdb Shift z [A]	0.0
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0

-fm details

Value	Description
0	display nothing
1	one char amino acid name
2	three char amino acid name
4	chain identifier
8	sequence number
16	display any atom

-if format

chainIdertifier&sequenceNumber(R123) FlagMode circleRedius circlelinewidth fontsize

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

Example of options only essential

6/90 Page (Left bottom part)

Option -AS

Case: AS=5

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Option -shiftx

Case: shiftx=10

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Option -shifty

Case: shifty=10

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Option -shiftz

Case: shiftz=1

6/90 Page

Option -dist

Case: dist=3

5/90 Page

Option -zmin

Case: zmin=1

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Option -zmax

Case: zmax=15

6/15 Page

Option -r

Case: r=0.5

6/90 Page

Option -plw

Case: plw=0.3

6/90 Page

Option -fontsize

Case: fontsize=1

6/90 Page

Option -fm

Case: fm=0

6/90 Page

Case: fm=1

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Case: fm=2

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Case: fm=4

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Case: fm=8

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Case: fm=16

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Option -if

A28 0 2.0 0.3 2
A147 1 0.5 0.3 4
A114 2 1.0 0.3 1
A128 4 1.0 0.3 4
A8 8 1.0 0.3 4
A56 16 0.5 0.3 4
A39 31 0.7 0.3 3

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