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From: Ramiro T. S. <urc...@gm...> - 2010-09-23 09:05:42
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Hi everyone and thanks for reading this! I am interested in measuring the angle between aromatic ring planes. Is there any easy way/script to do it? One way that came to my mind is creating a pseudoatom representing the centroid for each ring (I already know how to do that), then drawing two lines perpendicularly to the planes from both centroids, and finally measuring the angle between the lines. Will that be possible? How could this be done? Is there any other way? I'm completely clueless. Any help will be greatly appreciated. Thanks in advance, Ramiro Tellez Sanz Dept. Physical Chemistry University of Almeria Spain |
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From: Ramiro T. S. <urc...@gm...> - 2010-09-23 09:00:39
|
Hi everyone and thanks for reading this! I am interested in measuring the angle between aromatic ring planes. Is there any easy way/script to do it? One way that came to my mind is creating a pseudoatom representing the centroid for each ring (I already know how to do that), then drawing two lines perpendicularly to the planes from both centroids, and finally measuring the angle between the lines. Will that be possible? How could this be done? Is there any other way? I'm completely clueless. Any help will be greatly appreciated. Thanks in advance, Ramiro Tellez Sanz Dept. Physical Chemistry University of Almeria Spain |
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From: Tsjerk W. <ts...@gm...> - 2010-09-23 09:40:43
|
Hi Ramiro, Assuming your rings are nicely planar, and representing the ring as: 1-2-3 | | 6-5-4 you can get the plane normal vector as the vector cross product from (3)-(1) and (5)-(1). Doing so for both rings gives you the two normal vectors. The angle then follows from the dot product of the (normalized) normal vectors: angle = acos(n1 . n2) It becomes a bit more elaborate if the planes are not planar :) Hope it helps, Tsjerk On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz <urc...@gm...> wrote: > > > Hi everyone and thanks for reading this! > > I am interested in measuring the angle between aromatic ring planes. > Is there any easy way/script to do it? > > One way that came to my mind is creating a pseudoatom representing the > centroid for each ring (I already know how to do that), then drawing two > lines perpendicularly to the planes from both centroids, and finally > measuring the angle between the lines. Will that be possible? How could > this be done? > > Is there any other way? I'm completely clueless. Any help will be > greatly appreciated. > > Thanks in advance, > > Ramiro Tellez Sanz > Dept. Physical Chemistry > University of Almeria > Spain > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands |
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From: Ramiro T. S. <urc...@gm...> - 2010-09-23 10:19:27
|
Thanks for your kind help, Tsjerk. > Hi Ramiro, > > Assuming your rings are nicely planar, and representing the ring as: > > 1-2-3 > | | > 6-5-4 > > you can get the plane normal vector as the vector cross product from > (3)-(1) and (5)-(1). OK. But I just started to use pymol. Which are the commands to do so? I know how to get the coordinates of a selected atom, but need the pymol commands to treat the data: a) How to create the vectors from 1->3 and from 1->5 b) How to treat the vectors to perform the vector cross product > Doing so for both rings gives you the two normal vectors. The angle > then follows from the dot product of the (normalized) normal vectors: > > angle = acos(n1 . n2) Again, I would need the commands to: c) Normalize the vectors (how to set their modules = 1) I also guess n1 and n2 represent the normalized vectors, don't they? So this command is very clear :) > It becomes a bit more elaborate if the planes are not planar :) > > Hope it helps, > > Tsjerk Again, thanks very much in advance for your kind help. > On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz > <urc...@gm...> wrote: >> >> Hi everyone and thanks for reading this! >> >> I am interested in measuring the angle between aromatic ring planes. >> Is there any easy way/script to do it? >> >> One way that came to my mind is creating a pseudoatom representing the >> centroid for each ring (I already know how to do that), then drawing two >> lines perpendicularly to the planes from both centroids, and finally >> measuring the angle between the lines. Will that be possible? How could >> this be done? >> >> Is there any other way? I'm completely clueless. Any help will be >> greatly appreciated. >> >> Thanks in advance, >> >> Ramiro Tellez Sanz >> Dept. Physical Chemistry >> University of Almeria >> Spain >> >> >> ------------------------------------------------------------------------------ >> Start uncovering the many advantages of virtual appliances >> and start using them to simplify application deployment and >> accelerate your shift to cloud computing. >> http://p.sf.net/sfu/novell-sfdev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > |
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From: Tsjerk W. <ts...@gm...> - 2010-09-23 11:02:13
|
Hi Ramiro,
A bit of linear algebra wouldn't hurt... :p
In python:
def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
def svmul(s,a): return s*a[0], s*a[1], s*a[2]
def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
def cross(a,b): return a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2],
a[0]*b[1]-a[1]*b[0]
a = cmd.get_model('r. phe and i. ##RESIDUE1## and n. cg,ce1,ce2').atom
a = [ i.coord for i in a ]
b = cmd.get_model('r. phe and i. ##RESIDUE2## and n. cg,ce1,ce2').atom
b = [ i.coord for i in b ]
na = normalize(cross(vsub(a[1],a[0]),vsub(a[2],a[0])))
nb = normalize(cross(vsub(b[1],b[0]),vsub(b[2],b[0])))
angle = math.acos(dot(na,nb))
print angle
###
Haven't tested it, and there may be more efficient ways of getting the
coordinates. If you run into problems like this more often, it's
likely that you should pick up on algebra and programming... :)
Have fun,
Tsjerk
On Thu, Sep 23, 2010 at 12:19 PM, Ramiro Téllez Sanz
<urc...@gm...> wrote:
> Thanks for your kind help, Tsjerk.
>
>> Hi Ramiro,
>>
>> Assuming your rings are nicely planar, and representing the ring as:
>>
>> 1-2-3
>> | |
>> 6-5-4
>>
>> you can get the plane normal vector as the vector cross product from
>> (3)-(1) and (5)-(1).
>
> OK. But I just started to use pymol. Which are the commands to do so?
> I know how to get the coordinates of a selected atom, but need the pymol
> commands to treat the data:
> a) How to create the vectors from 1->3 and from 1->5
> b) How to treat the vectors to perform the vector cross product
>
>> Doing so for both rings gives you the two normal vectors. The angle
>> then follows from the dot product of the (normalized) normal vectors:
>>
>> angle = acos(n1 . n2)
>
> Again, I would need the commands to:
> c) Normalize the vectors (how to set their modules = 1)
>
> I also guess n1 and n2 represent the normalized vectors, don't they? So
> this command is very clear :)
>
>> It becomes a bit more elaborate if the planes are not planar :)
>>
>> Hope it helps,
>>
>> Tsjerk
>
> Again, thanks very much in advance for your kind help.
>
>> On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz
>> <urc...@gm...> wrote:
>>>
>>> Hi everyone and thanks for reading this!
>>>
>>> I am interested in measuring the angle between aromatic ring planes.
>>> Is there any easy way/script to do it?
>>>
>>> One way that came to my mind is creating a pseudoatom representing the
>>> centroid for each ring (I already know how to do that), then drawing two
>>> lines perpendicularly to the planes from both centroids, and finally
>>> measuring the angle between the lines. Will that be possible? How could
>>> this be done?
>>>
>>> Is there any other way? I'm completely clueless. Any help will be
>>> greatly appreciated.
>>>
>>> Thanks in advance,
>>>
>>> Ramiro Tellez Sanz
>>> Dept. Physical Chemistry
>>> University of Almeria
>>> Spain
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Start uncovering the many advantages of virtual appliances
>>> and start using them to simplify application deployment and
>>> accelerate your shift to cloud computing.
>>> http://p.sf.net/sfu/novell-sfdev2dev
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>
>>
>
>
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands
|
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From: Thomas H. <sp...@us...> - 2010-09-23 11:33:54
|
no need to implement common linear algebra functions, there is the
chempy.cpv module shipped with pymol (and there is numpy as well).
Ramiro, I recently did something similar, just adjust the residue
selection in the code below (requires numpy):
python
from chempy import cpv
import numpy, math
def plane_normal(selection):
stored.x = list()
cmd.iterate_state(-1, selection, 'stored.x.append([x,y,z])')
x = numpy.array(stored.x)
U,s,Vh = numpy.linalg.svd(x - x.mean(0))
return cpv.normalize(Vh[2])
dir1 = plane_normal('A/37/CG+CD1+CE1+CZ+CE2+CD2')
dir2 = plane_normal('A/41/CG+CD1+CE1+CZ+CE2+CD2')
print 'Angle in degrees:', math.degrees(cpv.get_angle(dir1, dir2))
python end
Cheers,
Thomas
On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
> Hi Ramiro,
>
> A bit of linear algebra wouldn't hurt... :p
> In python:
>
> def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
>
> def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
>
> def svmul(s,a): return s*a[0], s*a[1], s*a[2]
>
> def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
>
> def cross(a,b): return a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2],
> a[0]*b[1]-a[1]*b[0]
>
> a = cmd.get_model('r. phe and i. ##RESIDUE1## and n. cg,ce1,ce2').atom
> a = [ i.coord for i in a ]
> b = cmd.get_model('r. phe and i. ##RESIDUE2## and n. cg,ce1,ce2').atom
> b = [ i.coord for i in b ]
>
> na = normalize(cross(vsub(a[1],a[0]),vsub(a[2],a[0])))
> nb = normalize(cross(vsub(b[1],b[0]),vsub(b[2],b[0])))
> angle = math.acos(dot(na,nb))
>
> print angle
>
> ###
>
> Haven't tested it, and there may be more efficient ways of getting the
> coordinates. If you run into problems like this more often, it's
> likely that you should pick up on algebra and programming... :)
>
> Have fun,
>
> Tsjerk
>
>
> On Thu, Sep 23, 2010 at 12:19 PM, Ramiro Téllez Sanz
> <urc...@gm...> wrote:
> > Thanks for your kind help, Tsjerk.
> >
> >> Hi Ramiro,
> >>
> >> Assuming your rings are nicely planar, and representing the ring as:
> >>
> >> 1-2-3
> >> | |
> >> 6-5-4
> >>
> >> you can get the plane normal vector as the vector cross product from
> >> (3)-(1) and (5)-(1).
> >
> > OK. But I just started to use pymol. Which are the commands to do so?
> > I know how to get the coordinates of a selected atom, but need the pymol
> > commands to treat the data:
> > a) How to create the vectors from 1->3 and from 1->5
> > b) How to treat the vectors to perform the vector cross product
> >
> >> Doing so for both rings gives you the two normal vectors. The angle
> >> then follows from the dot product of the (normalized) normal vectors:
> >>
> >> angle = acos(n1 . n2)
> >
> > Again, I would need the commands to:
> > c) Normalize the vectors (how to set their modules = 1)
> >
> > I also guess n1 and n2 represent the normalized vectors, don't they? So
> > this command is very clear :)
> >
> >> It becomes a bit more elaborate if the planes are not planar :)
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >
> > Again, thanks very much in advance for your kind help.
> >
> >> On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz
> >> <urc...@gm...> wrote:
> >>>
> >>> Hi everyone and thanks for reading this!
> >>>
> >>> I am interested in measuring the angle between aromatic ring planes.
> >>> Is there any easy way/script to do it?
> >>>
> >>> One way that came to my mind is creating a pseudoatom representing the
> >>> centroid for each ring (I already know how to do that), then drawing two
> >>> lines perpendicularly to the planes from both centroids, and finally
> >>> measuring the angle between the lines. Will that be possible? How could
> >>> this be done?
> >>>
> >>> Is there any other way? I'm completely clueless. Any help will be
> >>> greatly appreciated.
> >>>
> >>> Thanks in advance,
> >>>
> >>> Ramiro Tellez Sanz
> >>> Dept. Physical Chemistry
> >>> University of Almeria
> >>> Spain
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> Groningen Institute for Biomolecular Research and Biotechnology /
> University of Groningen
> The Netherlands
--
Thomas Holder
Group of Steffen Schmidt
Department of Biochemistry
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
|
|
From: Tsjerk W. <ts...@gm...> - 2010-09-23 12:12:09
|
Hi Thomas,
You're right, and using an svd on the whole ring is also more correct.
But the vector stuff is simple and handy to have lying around, and it
serves also to give some insight in what's going on :)
numpy.linalg.svd is magic if you don't know how a cross product or
normalization works... So, now to make it a function taking two ring
bearing residues as arguments:
def ring_angle(selection1, selection2):
a = plane_normal(selection1 + " and not (e. h or n. c,n,ca,cb,o)")
b = plane_normal(selection2 + " and not (e. h or n. c,n,ca,cb,o)")
return math.degrees(cpv.get_angle(a, b))
cmd.extend("ring_angle",ring_angle)
Ramiro, do we need to write the methods section for the manuscript too? :p
Cheerio :)
Tsjerk
On Thu, Sep 23, 2010 at 1:33 PM, Thomas Holder
<sp...@us...> wrote:
> no need to implement common linear algebra functions, there is the
> chempy.cpv module shipped with pymol (and there is numpy as well).
>
> Ramiro, I recently did something similar, just adjust the residue
> selection in the code below (requires numpy):
>
> python
> from chempy import cpv
> import numpy, math
> def plane_normal(selection):
> stored.x = list()
> cmd.iterate_state(-1, selection, 'stored.x.append([x,y,z])')
> x = numpy.array(stored.x)
> U,s,Vh = numpy.linalg.svd(x - x.mean(0))
> return cpv.normalize(Vh[2])
> dir1 = plane_normal('A/37/CG+CD1+CE1+CZ+CE2+CD2')
> dir2 = plane_normal('A/41/CG+CD1+CE1+CZ+CE2+CD2')
> print 'Angle in degrees:', math.degrees(cpv.get_angle(dir1, dir2))
> python end
>
> Cheers,
> Thomas
>
> On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
>> Hi Ramiro,
>>
>> A bit of linear algebra wouldn't hurt... :p
>> In python:
>>
>> def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
>>
>> def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
>>
>> def svmul(s,a): return s*a[0], s*a[1], s*a[2]
>>
>> def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
>>
>> def cross(a,b): return a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2],
>> a[0]*b[1]-a[1]*b[0]
>>
>> a = cmd.get_model('r. phe and i. ##RESIDUE1## and n. cg,ce1,ce2').atom
>> a = [ i.coord for i in a ]
>> b = cmd.get_model('r. phe and i. ##RESIDUE2## and n. cg,ce1,ce2').atom
>> b = [ i.coord for i in b ]
>>
>> na = normalize(cross(vsub(a[1],a[0]),vsub(a[2],a[0])))
>> nb = normalize(cross(vsub(b[1],b[0]),vsub(b[2],b[0])))
>> angle = math.acos(dot(na,nb))
>>
>> print angle
>>
>> ###
>>
>> Haven't tested it, and there may be more efficient ways of getting the
>> coordinates. If you run into problems like this more often, it's
>> likely that you should pick up on algebra and programming... :)
>>
>> Have fun,
>>
>> Tsjerk
>>
>>
>> On Thu, Sep 23, 2010 at 12:19 PM, Ramiro Téllez Sanz
>> <urc...@gm...> wrote:
>> > Thanks for your kind help, Tsjerk.
>> >
>> >> Hi Ramiro,
>> >>
>> >> Assuming your rings are nicely planar, and representing the ring as:
>> >>
>> >> 1-2-3
>> >> | |
>> >> 6-5-4
>> >>
>> >> you can get the plane normal vector as the vector cross product from
>> >> (3)-(1) and (5)-(1).
>> >
>> > OK. But I just started to use pymol. Which are the commands to do so?
>> > I know how to get the coordinates of a selected atom, but need the pymol
>> > commands to treat the data:
>> > a) How to create the vectors from 1->3 and from 1->5
>> > b) How to treat the vectors to perform the vector cross product
>> >
>> >> Doing so for both rings gives you the two normal vectors. The angle
>> >> then follows from the dot product of the (normalized) normal vectors:
>> >>
>> >> angle = acos(n1 . n2)
>> >
>> > Again, I would need the commands to:
>> > c) Normalize the vectors (how to set their modules = 1)
>> >
>> > I also guess n1 and n2 represent the normalized vectors, don't they? So
>> > this command is very clear :)
>> >
>> >> It becomes a bit more elaborate if the planes are not planar :)
>> >>
>> >> Hope it helps,
>> >>
>> >> Tsjerk
>> >
>> > Again, thanks very much in advance for your kind help.
>> >
>> >> On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz
>> >> <urc...@gm...> wrote:
>> >>>
>> >>> Hi everyone and thanks for reading this!
>> >>>
>> >>> I am interested in measuring the angle between aromatic ring planes.
>> >>> Is there any easy way/script to do it?
>> >>>
>> >>> One way that came to my mind is creating a pseudoatom representing the
>> >>> centroid for each ring (I already know how to do that), then drawing two
>> >>> lines perpendicularly to the planes from both centroids, and finally
>> >>> measuring the angle between the lines. Will that be possible? How could
>> >>> this be done?
>> >>>
>> >>> Is there any other way? I'm completely clueless. Any help will be
>> >>> greatly appreciated.
>> >>>
>> >>> Thanks in advance,
>> >>>
>> >>> Ramiro Tellez Sanz
>> >>> Dept. Physical Chemistry
>> >>> University of Almeria
>> >>> Spain
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> Groningen Institute for Biomolecular Research and Biotechnology /
>> University of Groningen
>> The Netherlands
> --
> Thomas Holder
> Group of Steffen Schmidt
> Department of Biochemistry
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
|
|
From: Ramiro T. S. <urc...@gm...> - 2010-09-23 12:04:03
|
Thanks very much Thomas for your help.
> no need to implement common linear algebra functions, there is the
> chempy.cpv module shipped with pymol (and there is numpy as well).
>
> Ramiro, I recently did something similar, just adjust the residue
> selection in the code below (requires numpy):
>
I have pymol compiled with numpy support, so I have everyhting needed.
However, please excuse my ignorance in this matter, as I'm just
beginning to use pymol and have some basic questions:
* How do I adjust the code with my selected rings? Do I need to include
both residues in the same selection in pymol, then rename the selection,
and then include the chosen selection name in the code where you write
"selection"?
* How do I run the code after I adjust it with my "selection"? I have
never run a python program from within pymol. What should I do?
Thanks in advance.
> python
> from chempy import cpv
> import numpy, math
> def plane_normal(selection):
> stored.x = list()
> cmd.iterate_state(-1, selection, 'stored.x.append([x,y,z])')
> x = numpy.array(stored.x)
> U,s,Vh = numpy.linalg.svd(x - x.mean(0))
> return cpv.normalize(Vh[2])
> dir1 = plane_normal('A/37/CG+CD1+CE1+CZ+CE2+CD2')
> dir2 = plane_normal('A/41/CG+CD1+CE1+CZ+CE2+CD2')
> print 'Angle in degrees:', math.degrees(cpv.get_angle(dir1, dir2))
> python end
>
> Cheers,
> Thomas
>
> On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
>> Hi Ramiro,
>>
>> A bit of linear algebra wouldn't hurt... :p
>> In python:
>>
>> def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
>>
>> def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
>>
>> def svmul(s,a): return s*a[0], s*a[1], s*a[2]
>>
>> def normalize(a): return svmul(1/math.sqrt(dot(a,a)),a)
>>
>> def cross(a,b): return a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2],
>> a[0]*b[1]-a[1]*b[0]
>>
>> a = cmd.get_model('r. phe and i. ##RESIDUE1## and n. cg,ce1,ce2').atom
>> a = [ i.coord for i in a ]
>> b = cmd.get_model('r. phe and i. ##RESIDUE2## and n. cg,ce1,ce2').atom
>> b = [ i.coord for i in b ]
>>
>> na = normalize(cross(vsub(a[1],a[0]),vsub(a[2],a[0])))
>> nb = normalize(cross(vsub(b[1],b[0]),vsub(b[2],b[0])))
>> angle = math.acos(dot(na,nb))
>>
>> print angle
>>
>> ###
>>
>> Haven't tested it, and there may be more efficient ways of getting the
>> coordinates. If you run into problems like this more often, it's
>> likely that you should pick up on algebra and programming... :)
>>
>> Have fun,
>>
>> Tsjerk
>>
>>
>> On Thu, Sep 23, 2010 at 12:19 PM, Ramiro Téllez Sanz
>> <urc...@gm...> wrote:
>>> Thanks for your kind help, Tsjerk.
>>>
>>>> Hi Ramiro,
>>>>
>>>> Assuming your rings are nicely planar, and representing the ring as:
>>>>
>>>> 1-2-3
>>>> | |
>>>> 6-5-4
>>>>
>>>> you can get the plane normal vector as the vector cross product from
>>>> (3)-(1) and (5)-(1).
>>> OK. But I just started to use pymol. Which are the commands to do so?
>>> I know how to get the coordinates of a selected atom, but need the pymol
>>> commands to treat the data:
>>> a) How to create the vectors from 1->3 and from 1->5
>>> b) How to treat the vectors to perform the vector cross product
>>>
>>>> Doing so for both rings gives you the two normal vectors. The angle
>>>> then follows from the dot product of the (normalized) normal vectors:
>>>>
>>>> angle = acos(n1 . n2)
>>> Again, I would need the commands to:
>>> c) Normalize the vectors (how to set their modules = 1)
>>>
>>> I also guess n1 and n2 represent the normalized vectors, don't they? So
>>> this command is very clear :)
>>>
>>>> It becomes a bit more elaborate if the planes are not planar :)
>>>>
>>>> Hope it helps,
>>>>
>>>> Tsjerk
>>> Again, thanks very much in advance for your kind help.
>>>
>>>> On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz
>>>> <urc...@gm...> wrote:
>>>>> Hi everyone and thanks for reading this!
>>>>>
>>>>> I am interested in measuring the angle between aromatic ring planes.
>>>>> Is there any easy way/script to do it?
>>>>>
>>>>> One way that came to my mind is creating a pseudoatom representing the
>>>>> centroid for each ring (I already know how to do that), then drawing two
>>>>> lines perpendicularly to the planes from both centroids, and finally
>>>>> measuring the angle between the lines. Will that be possible? How could
>>>>> this be done?
>>>>>
>>>>> Is there any other way? I'm completely clueless. Any help will be
>>>>> greatly appreciated.
>>>>>
>>>>> Thanks in advance,
>>>>>
>>>>> Ramiro Tellez Sanz
>>>>> Dept. Physical Chemistry
>>>>> University of Almeria
>>>>> Spain
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> Groningen Institute for Biomolecular Research and Biotechnology /
>> University of Groningen
>> The Netherlands
|
|
From: Thomas H. <sp...@us...> - 2010-09-23 13:21:40
Attachments:
ring_angle.py
|
Hi Ramiro, > * How do I adjust the code with my selected rings? Do I need to include > both residues in the same selection in pymol, then rename the selection, > and then include the chosen selection name in the code where you write > "selection"? you need two selections of two residues, in my example the part 'A/37/CG +CD1+CE1+CZ+CE2+CD2' is the selection on chain A, residue 37 and ring atoms. > * How do I run the code after I adjust it with my "selection"? I have > never run a python program from within pymol. What should I do? I put the code (including Tsjerk's additions!) to a file, see attached. You have to run it with pymol (File > Run...) and then call the ring_angle command. Example to get angle between aromatic residues 37 and 41 in chain A: ring_angle chain A and resi 37, chain A and resi 41 Cheers, Thomas |
|
From: Jason V. <jas...@sc...> - 2010-09-23 13:55:17
|
Hi Ramiro, Another option is to fit (in a least-squares sense) a plane to each of your rings and then calculate the angle between the fitted planes' normals. This would help if your rings are not perfectly planar: it would spread the deviation among all atoms in the ring not just the ones you selected for the crossproduct. Cameron Mura created an excellent example of this in our PLoS article's supplementary information, posted on the PyMOLWiki http://www.pymolwiki.org/index.php/PLoS#Case_6:_Higher-order_structures.28.E2.89.A5_intermediate.2Fadvanced.29 The article is all about biomolecular graphics. Cheers, -- Jason On Thu, Sep 23, 2010 at 4:53 AM, Ramiro Téllez Sanz <urc...@gm...> wrote: > > > Hi everyone and thanks for reading this! > > I am interested in measuring the angle between aromatic ring planes. > Is there any easy way/script to do it? > > One way that came to my mind is creating a pseudoatom representing the > centroid for each ring (I already know how to do that), then drawing two > lines perpendicularly to the planes from both centroids, and finally > measuring the angle between the lines. Will that be possible? How could > this be done? > > Is there any other way? I'm completely clueless. Any help will be > greatly appreciated. > > Thanks in advance, > > Ramiro Tellez Sanz > Dept. Physical Chemistry > University of Almeria > Spain > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
|
From: Thomas H. <sp...@us...> - 2010-09-23 14:19:51
|
On Thu, 2010-09-23 at 09:54 -0400, Jason Vertrees wrote: > Hi Ramiro, > > Another option is to fit (in a least-squares sense) a plane to each of > your rings and then calculate the angle between the fitted planes' > normals. that's what the recently posted ring_angle.py script does. Cheers, Thomas |
