VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Thu Jun 18 2009 - 15:36:13 CDT

sorry for the typo...

set Sel [atomselect top all]
$Sel moveby [list $X0 $Y0 $Z0]
lappend M [list $a1 $b1 $c1]
lappend M [list $a2 $b2 $c2]
lappend M [list $a3 $b3 $c3]
set M [trans_from_rotate $M]
$Sel move $M

> Thanks buddy. That should work but I can find faster ways around,
> like doing the translation to the geometric center and then the
> rotation (which is actually what I do now):
>
> set Sel [atomselect top all]
> $Sel moveby [list $X0 $Y0 $Z0]
> lappend qM [list $a1 $b1 $c1]
> lappend qM [list $a2 $b2 $c2]
> lappend qM [list $a3 $b3 $c3]
> set M [trans_from_rotate $M]
> $Sel move $M
>
> I'm just curious to know how to do it with a 4x4 matrix directly.
>
> Tom
>
>> You could map the coordinates using the "set" command. You would
>> need to, e.g., load the molecule twice, changing the coordinates of
>> one based on the other. It would approximately work like this:
>>
>> set sel [atomselect 0 all]
>>
>> foreach ind [$sel get index] {
>> set temp1 [atomselect 0 "index $ind"]
>> set temp2 [atomselect 1 "index $ind"]
>> $temp2 set x [expr -0.79814*([$temp1 get x]-99.4985) +
>> -0.50649*([$temp1 get y]-55.308) + 0.32625*([$temp1 get z]-26.91025)]
>> $temp2 set y [expr ....]
>> $temp2 set z [expr ....]
>> $temp1 delete
>> $temp2 delete
>> }
>>
>> You could also do the mapping in place (only loading one structure)
>> by using intermediate variables for the new coordinates before
>> setting them.
>>
>> The 4x4 transformation matrix you are using is composed of a 3x3
>> rotation matrix and a translation vector (with the last row being
>> as you have given it), so it might take some work to determine it
>> for the transformation you want.
>>
>>
>> On Jun 18, 2009, at 2:55 AM, Thomas Evangelidis wrote:
>>
>>> Dear VMD users,
>>>
>>> I have the new coordinates of a protein in the following form:
>>>
>>> X2 = -0.79814*(X1-99.4985) + -0.50649*(Y1-55.308) +
>>> -0.32625*(Z1-26.91025)
>>> Y2 = 0.40972*(X1-99.4985) + -0.85333*(Y1-55.308) +
>>> 0.32243*(Z1-26.91025)
>>> Z2 = -0.44171*(X1-99.4985) + 0.12367*(Y1-55.308) +
>>> 0.88859*(Z1-26.91025)
>>>
>>> So I set the following matrix for the transformation:
>>>
>>> {{-0.79814 -0.50649 -0.32625 -99.4985} {0.40972 -0.85333 0.32243
>>> -55.308} {-0.44171 0.12367 0.88859 -26.91025} {0.0 0.0 0.0 1.0}}
>>>
>>> but the molecule is moved to a completely different location than
>>> the one it should be. I am confused, either the matrix or the
>>> coordinates are wrong. Can anyone shed some light on this please?
>>>
>>> thanks in advance,
>>> Tom
>>
>>
>
>
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>
>
>

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