Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation
Hi Lorenzo and Blaine,
There is a "set_bond" command which can set (some) settings for individual
bonds.
To change stick color and radius for the bond between atom 2 and 3:
set_bond stick_color, yellow, index 2, index 3
set_bond stick_radius, 0.2, index 2, index 3
Cheers,
Thomas
> On Dec 11, 2019, at 4:57 PM, Mooers, Blaine H.M. (HSC)
> wrote:
>
> Hi Lorenzo,
>
> The use the lines instead of sticks may reduce the anticipated hit on
> performance.
> There is a line_color setting that use you can.
>
> Best regards,
>
> Blaine
>
>
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Wednesday, December 11, 2019 9:48 AM
> To: Mooers, Blaine H.M. (HSC)
> Cc: pymol-users
> Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
> representation
>
> Hi Blaine,
>
> Yes, that's essentially what I'm doing. My worry is that since this doubles
> the amount of coordinates to keep track of, it will be detrimental to how
> long a trajectory I can load. Is there any other way to do this?
>
> On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC)
> mailto:blaine-moo...@ouhsc.edu>> wrote:
> Hi Lorenzo,
>
> You could make an object out of the elastic bonds with the 'create' command,
> show it as sticks, and use the stick_color setting to color the sticks only.
> You could make different objects for different subsets of the elastic bonds
> and color them differently.
>
> Here is an example of the 'create' command that I used to make an object out
> of six coordinate covalent bonds between a sodium, a N7 nitrogen of an
> adenine, and five waters.
>
> cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or
> resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
> cmd.set('stick_color','magenta','coorCov')
> cmd.show('sticks','coorCov')
>
> The color of the atoms, if shown as spheres, will remain the same.
> Although the above two commands are in the Python form, you can paste them
> onto the top command line in PyMOL.
>
> By specifying the object as your selection in the argument to the set
> command, you can also change the thickness of the sticks in only than object
> so
> you can have sticks of different thickness in the same scene.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Wednesday, December 11, 2019 8:38 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
> representation
>
> Dear pymol users,
>
> I'm trying to properly represent a coarse-grained protein model that has an
> elastic network.
>
> I would like to show the bonds that are part of the elastic network with a
> different color (and possibly representation) from the normal bonds between
> atoms. However, as far as I know, color settings are atom-based, so I wasn't
> able to do what I wanted, because all bonds that lead to an atom will always
> share the same color.
>
> The only solution I found was to create a copy of the protein with
> pseudoatoms and draw the elastic network there. However, I expect this has a
> negative effect on the performance, which is relevant since I plan to use
> this for molecular dynamics trajectories.
>
> Am I trying to do this the wrong way? Is it just unfeasible?
>
>
> ___
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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe:
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation
Hi Lorenzo,
The use the lines instead of sticks may reduce the anticipated hit on
performance.
There is a line_color setting that use you can.
Best regards,
Blaine
From: Lorenzo Gaifas [bris...@gmail.com]
Sent: Wednesday, December 11, 2019 9:48 AM
To: Mooers, Blaine H.M. (HSC)
Cc: pymol-users
Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
representation
Hi Blaine,
Yes, that's essentially what I'm doing. My worry is that since this doubles the
amount of coordinates to keep track of, it will be detrimental to how long a
trajectory I can load. Is there any other way to do this?
On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC)
mailto:blaine-moo...@ouhsc.edu>> wrote:
Hi Lorenzo,
You could make an object out of the elastic bonds with the 'create' command,
show it as sticks, and use the stick_color setting to color the sticks only.
You could make different objects for different subsets of the elastic bonds and
color them differently.
Here is an example of the 'create' command that I used to make an object out of
six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine,
and five waters.
cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi
319 or resi 419 or resi 519 or (resi 3 and name N7)))')
cmd.set('stick_color','magenta','coorCov')
cmd.show('sticks','coorCov')
The color of the atoms, if shown as spheres, will remain the same.
Although the above two commands are in the Python form, you can paste them onto
the top command line in PyMOL.
By specifying the object as your selection in the argument to the set command,
you can also change the thickness of the sticks in only than object so
you can have sticks of different thickness in the same scene.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Lorenzo Gaifas [bris...@gmail.com]
Sent: Wednesday, December 11, 2019 8:38 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
representation
Dear pymol users,
I'm trying to properly represent a coarse-grained protein model that has an
elastic network.
I would like to show the bonds that are part of the elastic network with a
different color (and possibly representation) from the normal bonds between
atoms. However, as far as I know, color settings are atom-based, so I wasn't
able to do what I wanted, because all bonds that lead to an atom will always
share the same color.
The only solution I found was to create a copy of the protein with pseudoatoms
and draw the elastic network there. However, I expect this has a negative
effect on the performance, which is relevant since I plan to use this for
molecular dynamics trajectories.
Am I trying to do this the wrong way? Is it just unfeasible?
___
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Unsubscribe:
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Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation
Hi Lorenzo,
You could make an object out of the elastic bonds with the 'create' command,
show it as sticks, and use the stick_color setting to color the sticks only.
You could make different objects for different subsets of the elastic bonds and
color them differently.
Here is an example of the 'create' command that I used to make an object out of
six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine,
and five waters.
cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi
319 or resi 419 or resi 519 or (resi 3 and name N7)))')
cmd.set('stick_color','magenta','coorCov')
cmd.show('sticks','coorCov')
The color of the atoms, if shown as spheres, will remain the same.
Although the above two commands are in the Python form, you can paste them onto
the top command line in PyMOL.
By specifying the object as your selection in the argument to the set command,
you can also change the thickness of the sticks in only than object so
you can have sticks of different thickness in the same scene.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
From: Lorenzo Gaifas [bris...@gmail.com]
Sent: Wednesday, December 11, 2019 8:38 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
representation
Dear pymol users,
I'm trying to properly represent a coarse-grained protein model that has an
elastic network.
I would like to show the bonds that are part of the elastic network with a
different color (and possibly representation) from the normal bonds between
atoms. However, as far as I know, color settings are atom-based, so I wasn't
able to do what I wanted, because all bonds that lead to an atom will always
share the same color.
The only solution I found was to create a copy of the protein with pseudoatoms
and draw the elastic network there. However, I expect this has a negative
effect on the performance, which is relevant since I plan to use this for
molecular dynamics trajectories.
Am I trying to do this the wrong way? Is it just unfeasible?
___
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Unsubscribe:
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Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation
Hi Blaine,
Yes, that's essentially what I'm doing. My worry is that since this doubles
the amount of coordinates to keep track of, it will be detrimental to how
long a trajectory I can load. Is there any other way to do this?
On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) <
blaine-moo...@ouhsc.edu> wrote:
> Hi Lorenzo,
>
> You could make an object out of the elastic bonds with the 'create'
> command, show it as sticks, and use the stick_color setting to color the
> sticks only.
> You could make different objects for different subsets of the elastic
> bonds and color them differently.
>
> Here is an example of the 'create' command that I used to make an object
> out of six coordinate covalent bonds between a sodium, a N7 nitrogen of an
> adenine, and five waters.
>
> cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or
> resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
> cmd.set('stick_color','magenta','coorCov')
> cmd.show('sticks','coorCov')
>
> The color of the atoms, if shown as spheres, will remain the same.
> Although the above two commands are in the Python form, you can paste them
> onto the top command line in PyMOL.
>
> By specifying the object as your selection in the argument to the set
> command, you can also change the thickness of the sticks in only than
> object so
> you can have sticks of different thickness in the same scene.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Wednesday, December 11, 2019 8:38 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
> representation
>
> Dear pymol users,
>
> I'm trying to properly represent a coarse-grained protein model that has
> an elastic network.
>
> I would like to show the bonds that are part of the elastic network with a
> different color (and possibly representation) from the normal bonds between
> atoms. However, as far as I know, color settings are atom-based, so I
> wasn't able to do what I wanted, because all bonds that lead to an atom
> will always share the same color.
>
> The only solution I found was to create a copy of the protein with
> pseudoatoms and draw the elastic network there. However, I expect this has
> a negative effect on the performance, which is relevant since I plan to use
> this for molecular dynamics trajectories.
>
> Am I trying to do this the wrong way? Is it just unfeasible?
>
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