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From: rainfieldcn <rai...@gm...> - 2014-09-24 22:36:12
|
Hi all, I generate two pseudoatoms "start_point" and "end_point" by center_of_mass.py. I load an object "tunnel" which has a sets of atoms in one chain. I want to measure the angle from each atoms in "tunnel" to "end_point" to "start_point". at the same time, I want to print the B-factor of atoms in "tunnel". To measure the angle, I programmed like this，but it doesn't work. I guess it's because get_angle function needs some particular variable format. By the way, how can I print the b factor of atom? Thanks, Lei from pymol import cmd, stored def vertical_distance( start_point, end_point, tunnel ): centers = cmd.get_model(tunnel,1) for a in centers.atom: angle= cmd.get_angle(start_point, end_point,a) print angle return (start_point, end_point, tunnel) cmd.extend( "vertical_distance", vertical_distance ); |
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From: Matthew B. <mp...@pi...> - 2014-09-24 22:52:44
|
Hi,
you can just use the 'angle' command.
cmd.angle('angle1', 'start_point', 'end_point', a)
To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')
HTH,
Matt Baumgartner
On 09/24/2014 06:35 PM, rainfieldcn wrote:
> Hi all,
> I generate two pseudoatoms "start_point" and "end_point" by
> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
> in one chain.
> I want to measure the angle from each atoms in "tunnel" to "end_point"
> to "start_point". at the same time, I want to print the B-factor of
> atoms in "tunnel".
> To measure the angle, I programmed like this，but it doesn't work.
> I guess it's because get_angle function needs some particular variable
> format.
> By the way, how can I print the b factor of atom?
> Thanks,
> Lei
>
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> centers = cmd.get_model(tunnel,1)
> for a in centers.atom:
> angle= cmd.get_angle(start_point, end_point,a)
> print angle
> return (start_point, end_point, tunnel)
> cmd.extend( "vertical_distance", vertical_distance );
>
>
>
>
>
>
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From: Sampson, J. <Jar...@ny...> - 2014-09-24 23:44:17
|
Hi Lei -
The `get_angle` command needs an atom selection for your “tunnel" atoms, which, like the B-factor as Matt mentioned, you can also get using `iterate`:
###
# create a list
stored.centers = []
# get the macro selection string for each atom in tunnel
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model, segi, chain, resn, resi, name))')
# loop through the list of centers and print each angle
for s in stored.centers:
angle = cmd.get_angle('start_point', 'end_point', s)
print "%s: %3.2f" % (s, angle)
###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...<mailto:mp...@pi...>> wrote:
Hi,
you can just use the 'angle' command.
cmd.angle('angle1', 'start_point', 'end_point', a)
To print the b-factor you can use the iterate command
(http://www.pymolwiki.org/index.php/Iterate)
cmd.iterate('(a)', 'print b')
HTH,
Matt Baumgartner
On 09/24/2014 06:35 PM, rainfieldcn wrote:
Hi all,
I generate two pseudoatoms "start_point" and "end_point" by
center_of_mass.py. I load an object "tunnel" which has a sets of atoms
in one chain.
I want to measure the angle from each atoms in "tunnel" to "end_point"
to "start_point". at the same time, I want to print the B-factor of
atoms in "tunnel".
To measure the angle, I programmed like this，but it doesn't work.
I guess it's because get_angle function needs some particular variable
format.
By the way, how can I print the b factor of atom?
Thanks,
Lei
from pymol import cmd, stored
def vertical_distance( start_point, end_point, tunnel ):
centers = cmd.get_model(tunnel,1)
for a in centers.atom:
angle= cmd.get_angle(start_point, end_point,a)
print angle
return (start_point, end_point, tunnel)
cmd.extend( "vertical_distance", vertical_distance );
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From: Lei C. <rai...@gm...> - 2014-09-25 03:27:34
|
Hi,
I still have trouble. I am not sure if it is because the tunnel pdb is
not standard. (it's an output file from another software called
CAVER.)
My tunnel pdb looks like:
ATOM 1 H FIL T 537 -44.636 -88.973 27.394 5.02
ATOM 2 H FIL T 537 -44.620 -88.474 27.363 4.90
CONECT 1 2
ATOM 3 H FIL T 537 -44.574 -87.982 27.350 4.82
CONECT 2 3
ATOM 4 H FIL T 537 -44.568 -87.484 27.315 4.78
CONECT 3 4
ATOM 5 H FIL T 537 -44.561 -86.985 27.279 4.78
CONECT 4 5
ATOM 6 H FIL T 537 -44.554 -86.486 27.243 4.82
CONECT 5 6
My codes：
from pymol import cmd, stored
def vertical_distance( start_point, end_point, tunnel ):
stored.centers = []
cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
(model, segi, chain, resn, resi, name))')
for s in stored.centers:
print s
angle = cmd.get_angle(start_point, end_point, s)
print "%s: %3.2f" % (s, angle)
cmd.extend( "vertical_distance", vertical_distance );
output:
/tunnel//T/FIL`537/H
GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
If I use cmd.angle, I get:
cmd-Error: The 'pk3' selection is undefined.
On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
> Hi Lei -
>
> The `get_angle` command needs an atom selection for your “tunnel" atoms,
> which, like the B-factor as Matt mentioned, you can also get using
> `iterate`:
>
> ###
>
> # create a list
> stored.centers = []
>
> # get the macro selection string for each atom in tunnel
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
> segi, chain, resn, resi, name))')
>
> # loop through the list of centers and print each angle
> for s in stored.centers:
> angle = cmd.get_angle('start_point', 'end_point', s)
> print "%s: %3.2f" % (s, angle)
>
> ###
>
> Hope that helps.
>
> Cheers,
> Jared
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>
> Hi,
> you can just use the 'angle' command.
>
> cmd.angle('angle1', 'start_point', 'end_point', a)
>
> To print the b-factor you can use the iterate command
> (http://www.pymolwiki.org/index.php/Iterate)
> cmd.iterate('(a)', 'print b')
>
> HTH,
> Matt Baumgartner
>
>
> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>
> Hi all,
> I generate two pseudoatoms "start_point" and "end_point" by
> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
> in one chain.
> I want to measure the angle from each atoms in "tunnel" to "end_point"
> to "start_point". at the same time, I want to print the B-factor of
> atoms in "tunnel".
> To measure the angle, I programmed like this，but it doesn't work.
> I guess it's because get_angle function needs some particular variable
> format.
> By the way, how can I print the b factor of atom?
> Thanks,
> Lei
>
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> centers = cmd.get_model(tunnel,1)
> for a in centers.atom:
> angle= cmd.get_angle(start_point, end_point,a)
> print angle
> return (start_point, end_point, tunnel)
> cmd.extend( "vertical_distance", vertical_distance );
>
>
>
>
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
> 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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> _______________________________________________
> 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: Gianluca S. <gia...@ib...> - 2014-09-25 08:01:50
|
It seems due to the fact that youre selection s is not a valid selection.
Try to simplify it by simply giving
(model, chain, resi, name)
It should be enough to define a single atom, as required by get_angle
On 9/25/14 5:27 AM, Lei Chen wrote:
> Hi,
> I still have trouble. I am not sure if it is because the tunnel pdb is
> not standard. (it's an output file from another software called
> CAVER.)
> My tunnel pdb looks like:
> ATOM 1 H FIL T 537 -44.636 -88.973 27.394 5.02
> ATOM 2 H FIL T 537 -44.620 -88.474 27.363 4.90
> CONECT 1 2
> ATOM 3 H FIL T 537 -44.574 -87.982 27.350 4.82
> CONECT 2 3
> ATOM 4 H FIL T 537 -44.568 -87.484 27.315 4.78
> CONECT 3 4
> ATOM 5 H FIL T 537 -44.561 -86.985 27.279 4.78
> CONECT 4 5
> ATOM 6 H FIL T 537 -44.554 -86.486 27.243 4.82
> CONECT 5 6
> My codes：
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> stored.centers = []
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
> (model, segi, chain, resn, resi, name))')
> for s in stored.centers:
> print s
> angle = cmd.get_angle(start_point, end_point, s)
> print "%s: %3.2f" % (s, angle)
> cmd.extend( "vertical_distance", vertical_distance );
>
> output:
> /tunnel//T/FIL`537/H
> GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
>
> If I use cmd.angle, I get:
> cmd-Error: The 'pk3' selection is undefined.
>
>
> On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
>> Hi Lei -
>>
>> The `get_angle` command needs an atom selection for your “tunnel" atoms,
>> which, like the B-factor as Matt mentioned, you can also get using
>> `iterate`:
>>
>> ###
>>
>> # create a list
>> stored.centers = []
>>
>> # get the macro selection string for each atom in tunnel
>> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
>> segi, chain, resn, resi, name))')
>>
>> # loop through the list of centers and print each angle
>> for s in stored.centers:
>> angle = cmd.get_angle('start_point', 'end_point', s)
>> print "%s: %3.2f" % (s, angle)
>>
>> ###
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>>
>>
>>
>> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>>
>> Hi,
>> you can just use the 'angle' command.
>>
>> cmd.angle('angle1', 'start_point', 'end_point', a)
>>
>> To print the b-factor you can use the iterate command
>> (http://www.pymolwiki.org/index.php/Iterate)
>> cmd.iterate('(a)', 'print b')
>>
>> HTH,
>> Matt Baumgartner
>>
>>
>> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>>
>> Hi all,
>> I generate two pseudoatoms "start_point" and "end_point" by
>> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
>> in one chain.
>> I want to measure the angle from each atoms in "tunnel" to "end_point"
>> to "start_point". at the same time, I want to print the B-factor of
>> atoms in "tunnel".
>> To measure the angle, I programmed like this，but it doesn't work.
>> I guess it's because get_angle function needs some particular variable
>> format.
>> By the way, how can I print the b factor of atom?
>> Thanks,
>> Lei
>>
>> from pymol import cmd, stored
>> def vertical_distance( start_point, end_point, tunnel ):
>> centers = cmd.get_model(tunnel,1)
>> for a in centers.atom:
>> angle= cmd.get_angle(start_point, end_point,a)
>> print angle
>> return (start_point, end_point, tunnel)
>> cmd.extend( "vertical_distance", vertical_distance );
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
>> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
>> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
>> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
>> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
>> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
>> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
>> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
>> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>>
>
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
--
Gianluca Santoni,
Dynamop Group
Institut de Biologie Structurale
6 rue Jules Horowitz
38027 Grenoble Cedex 1
France
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
|
|
From: Thomas H. <tho...@sc...> - 2014-09-25 11:26:21
|
Hi Lei,
those tunnel atoms all have the same name, thus the selection is not unique (not a *single* atom but multiple). For a script like that, it's best to select by atom index.
cmd.iterate("tunnel", 'stored.centers.append("(%s`%d)" % (model, index))')
Cheers,
Thomas
On 24 Sep 2014, at 23:27, Lei Chen <rai...@gm...> wrote:
> Hi,
> I still have trouble. I am not sure if it is because the tunnel pdb is
> not standard. (it's an output file from another software called
> CAVER.)
> My tunnel pdb looks like:
> ATOM 1 H FIL T 537 -44.636 -88.973 27.394 5.02
> ATOM 2 H FIL T 537 -44.620 -88.474 27.363 4.90
> CONECT 1 2
> ATOM 3 H FIL T 537 -44.574 -87.982 27.350 4.82
> CONECT 2 3
> ATOM 4 H FIL T 537 -44.568 -87.484 27.315 4.78
> CONECT 3 4
> ATOM 5 H FIL T 537 -44.561 -86.985 27.279 4.78
> CONECT 4 5
> ATOM 6 H FIL T 537 -44.554 -86.486 27.243 4.82
> CONECT 5 6
> My codes：
> from pymol import cmd, stored
> def vertical_distance( start_point, end_point, tunnel ):
> stored.centers = []
> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" %
> (model, segi, chain, resn, resi, name))')
> for s in stored.centers:
> print s
> angle = cmd.get_angle(start_point, end_point, s)
> print "%s: %3.2f" % (s, angle)
> cmd.extend( "vertical_distance", vertical_distance );
>
> output:
> /tunnel//T/FIL`537/H
> GetAngle-Error: Selection 3 doesn't contain a single atom/vertex.
>
> If I use cmd.angle, I get:
> cmd-Error: The 'pk3' selection is undefined.
>
>
> On Wed, Sep 24, 2014 at 4:44 PM, Sampson, Jared <Jar...@ny...> wrote:
>> Hi Lei -
>>
>> The `get_angle` command needs an atom selection for your “tunnel" atoms,
>> which, like the B-factor as Matt mentioned, you can also get using
>> `iterate`:
>>
>> ###
>>
>> # create a list
>> stored.centers = []
>>
>> # get the macro selection string for each atom in tunnel
>> cmd.iterate("tunnel", 'stored.centers.append("/%s/%s/%s/%s`%s/%s" % (model,
>> segi, chain, resn, resi, name))')
>>
>> # loop through the list of centers and print each angle
>> for s in stored.centers:
>> angle = cmd.get_angle('start_point', 'end_point', s)
>> print "%s: %3.2f" % (s, angle)
>>
>> ###
>>
>> Hope that helps.
>>
>> Cheers,
>> Jared
>>
>> --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>>
>>
>>
>> On Sep 24, 2014, at 6:52 PM, Matthew Baumgartner <mp...@pi...> wrote:
>>
>> Hi,
>> you can just use the 'angle' command.
>>
>> cmd.angle('angle1', 'start_point', 'end_point', a)
>>
>> To print the b-factor you can use the iterate command
>> (http://www.pymolwiki.org/index.php/Iterate)
>> cmd.iterate('(a)', 'print b')
>>
>> HTH,
>> Matt Baumgartner
>>
>>
>> On 09/24/2014 06:35 PM, rainfieldcn wrote:
>>
>> Hi all,
>> I generate two pseudoatoms "start_point" and "end_point" by
>> center_of_mass.py. I load an object "tunnel" which has a sets of atoms
>> in one chain.
>> I want to measure the angle from each atoms in "tunnel" to "end_point"
>> to "start_point". at the same time, I want to print the B-factor of
>> atoms in "tunnel".
>> To measure the angle, I programmed like this，but it doesn't work.
>> I guess it's because get_angle function needs some particular variable
>> format.
>> By the way, how can I print the b factor of atom?
>> Thanks,
>> Lei
>>
>> from pymol import cmd, stored
>> def vertical_distance( start_point, end_point, tunnel ):
>> centers = cmd.get_model(tunnel,1)
>> for a in centers.atom:
>> angle= cmd.get_angle(start_point, end_point,a)
>> print angle
>> return (start_point, end_point, tunnel)
>> cmd.extend( "vertical_distance", vertical_distance );
--
Thomas Holder
PyMOL Developer
Schrödinger, Inc.
|
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