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关于pdb文件的REMARK 290

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发表于 2009-2-12 17:33:00 | 显示全部楼层 |阅读模式
把一个单体pdb做成对应的高聚物,需要把单体旋转和平移到合适的位置,在pdb当中,这个平移是确定的,在REMARK290项当中给出。
而REMARK 350也给出了一个旋转矩阵。
这两个旋转矩阵有啥区别?
例:1J4N.pdb
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2
REMARK 290
REMARK 290SYMOPSYMMETRY
REMARK 290NNNMMMOPERATOR
REMARK 2901555X,Y,Z
REMARK 2902555-X,-Y,Z
REMARK 2903555-Y,X,Z
REMARK 2904555Y,-X,Z
REMARK 2905555-X,Y,-Z
REMARK 2906555X,-Y,-Z
REMARK 2907555Y,X,-Z
REMARK 2908555-Y,-X,-Z
REMARK 29095551/2+X,1/2+Y,1/2+Z
REMARK 290105551/2-X,1/2-Y,1/2+Z
REMARK 290115551/2-Y,1/2+X,1/2+Z
REMARK 290125551/2+Y,1/2-X,1/2+Z
REMARK 290135551/2-X,1/2+Y,1/2-Z
REMARK 290145551/2+X,1/2-Y,1/2-Z
REMARK 290155551/2+Y,1/2+X,1/2-Z
REMARK 290165551/2-Y,1/2-X,1/2-Z
REMARK 290
REMARK 290WHERE NNN -> OPERATOR NUMBER
REMARK 290MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290SMTRY111.0000000.0000000.0000000.00000
REMARK 290SMTRY210.0000001.0000000.0000000.00000
REMARK 290SMTRY310.0000000.0000001.0000000.00000
REMARK 290SMTRY12 -1.0000000.0000000.0000000.00000
REMARK 290SMTRY220.000000 -1.0000000.0000000.00000
REMARK 290SMTRY320.0000000.0000001.0000000.00000
REMARK 290SMTRY130.000000 -1.0000000.0000000.00000
REMARK 290SMTRY231.0000000.0000000.0000000.00000
REMARK 290SMTRY330.0000000.0000001.0000000.00000
REMARK 290SMTRY140.0000001.0000000.0000000.00000
REMARK 290SMTRY24 -1.0000000.0000000.0000000.00000
REMARK 290SMTRY340.0000000.0000001.0000000.00000
REMARK 290SMTRY15 -1.0000000.0000000.0000000.00000
REMARK 290SMTRY250.0000001.0000000.0000000.00000
REMARK 290SMTRY350.0000000.000000 -1.0000000.00000
REMARK 290SMTRY161.0000000.0000000.0000000.00000
REMARK 290SMTRY260.000000 -1.0000000.0000000.00000
REMARK 290SMTRY360.0000000.000000 -1.0000000.00000
REMARK 290SMTRY170.0000001.0000000.0000000.00000
REMARK 290SMTRY271.0000000.0000000.0000000.00000
REMARK 290SMTRY370.0000000.000000 -1.0000000.00000
REMARK 290SMTRY180.000000 -1.0000000.0000000.00000
REMARK 290SMTRY28 -1.0000000.0000000.0000000.00000
REMARK 290SMTRY380.0000000.000000 -1.0000000.00000
REMARK 290SMTRY191.0000000.0000000.00000046.66550
REMARK 290SMTRY290.0000001.0000000.00000046.66550
REMARK 290SMTRY390.0000000.0000001.00000090.24500
REMARK 290SMTRY110 -1.0000000.0000000.00000046.66550
REMARK 290SMTRY2100.000000 -1.0000000.00000046.66550
REMARK 290SMTRY3100.0000000.0000001.00000090.24500
REMARK 290SMTRY1110.000000 -1.0000000.00000046.66550
REMARK 290SMTRY2111.0000000.0000000.00000046.66550
REMARK 290SMTRY3110.0000000.0000001.00000090.24500
REMARK 290SMTRY1120.0000001.0000000.00000046.66550
REMARK 290SMTRY212 -1.0000000.0000000.00000046.66550
REMARK 290SMTRY3120.0000000.0000001.00000090.24500
REMARK 290SMTRY113 -1.0000000.0000000.00000046.66550
REMARK 290SMTRY2130.0000001.0000000.00000046.66550
REMARK 290SMTRY3130.0000000.000000 -1.00000090.24500
REMARK 290SMTRY1141.0000000.0000000.00000046.66550
REMARK 290SMTRY2140.000000 -1.0000000.00000046.66550
REMARK 290SMTRY3140.0000000.000000 -1.00000090.24500
REMARK 290SMTRY1150.0000001.0000000.00000046.66550
REMARK 290SMTRY2151.0000000.0000000.00000046.66550
REMARK 290SMTRY3150.0000000.000000 -1.00000090.24500
REMARK 290SMTRY1160.000000 -1.0000000.00000046.66550
REMARK 290SMTRY216 -1.0000000.0000000.00000046.66550
REMARK 290SMTRY3160.0000000.000000 -1.00000090.24500
REMARK 290
REMARK 290 REMARK: NULL
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350BIOMT111.0000000.0000000.0000000.00000
REMARK 350BIOMT210.0000001.0000000.0000000.00000
REMARK 350BIOMT310.0000000.0000001.0000000.00000
REMARK 350BIOMT12 -1.0000000.0000000.00000093.33100
REMARK 350BIOMT220.000000 -1.0000000.00000093.33100
REMARK 350BIOMT320.0000000.0000001.0000000.00000
REMARK 350BIOMT130.000000 -1.0000000.00000093.33100
REMARK 350BIOMT231.0000000.0000000.0000000.00000
REMARK 350BIOMT330.0000000.0000001.0000000.00000
REMARK 350BIOMT140.0000001.0000000.0000000.00000
REMARK 350BIOMT24 -1.0000000.0000000.00000093.33100
REMARK 350BIOMT340.0000000.0000001.0000000.00000
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 楼主| 发表于 2009-2-15 15:57:00 | 显示全部楼层
嗯,REMARK 290仍然不知道是什么东西,但是REMARK 350是从单体生成高聚物的对称矩阵,前面3X3是旋转矩阵,后面3X1是平移矩阵。
我在用这个矩阵的时候还犯了一个错误,就是这个3X3矩阵是针对3X1向量矩阵而不是1X3向量矩阵的:

REMARK 350BIOMT130.000000 -1.0000000.00000093.33100
REMARK 350BIOMT231.0000000.0000000.0000000.00000
REMARK 350BIOMT330.0000000.0000001.0000000.00000
用这个矩阵应该是这样的:
0 -1 0x93.393.3-y
10 0X y +0=x
00 1z0z
而不是
0 -1 0
(x, y, z)X 10 0 +(93.3, 0, 0)=(93.3+y,-x,z)
00 1
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 楼主| 发表于 2009-2-15 17:43:00 | 显示全部楼层
用move,需要给出一个4X4矩阵,这个矩阵虽然可以用trans生成,但是不知道如何与pdb提供的矩阵互相转换。
用来做坐标的矩阵变换的VMD脚本:
proc mol_rotate {matrix matrixb mole} {;#$matrix is the 3X3 rotation matrix; while $matrixb is the 3X1 translation matrix; and the $mole is the atomselection that needs to be treated.
for {set i 0} {$i < 3} {incr i 1} {
set row [lindex $matrix $i]
for {set j 0} {$j < 3} {incr j 1} {
set mat($i,$j) [lindex $row $j]
}
};#hence we get $mat which is a 3X3 array representing $matrix
set coordnate [$mole get {x y z}];#$coordnate is a list made up of many {x y z} entries.
foreach {posi} $coordnate {;#posi should be the coordnate vector {x y z} of current atom.
foreach {x y z} $posi {;#$x $y $z are the x y z of current atom.
set xn [expr $x*$mat(0,0)+$y*$mat(0,1)+$z*$mat(0,2)]
set yn [expr $x*$mat(1,0)+$y*$mat(1,1)+$z*$mat(1,2)]
set zn [expr $x*$mat(2,0)+$y*$mat(2,1)+$z*$mat(2,2)]
}
lappend newx [expr $xn+[lindex $matrixb 0]]
lappend newy [expr $yn+[lindex $matrixb 1]]
lappend newz [expr $zn+[lindex $matrixb 2]]
}
$mole set x $newx
$mole set y $newy
$mole set z $newz
#$mole writepdb "$mole.pdb"
}
mol load pdb monomer.pdb
mol load pdb monomer.pdb
mol load pdb monomer.pdb
set MONA [atomselect 0 "all"]
set matrix1 [list {-1 0 0} {0 -1 0} {0 0 1}]
set matrix1b [list 93 93 0]
mol_rotate $matrix1 $matrix1b $MONA
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