Re: [PyMOL] feature request
Hi Jared and Vaheh - We've implemented two modes and pushed the change to the github repository. set internal_gui_name_color_mode, set internal_gui_name_color_mode, 2 Mode 1 is color by first carbon color. We think this is the most relevant use case and what the user typically would expect. This only affects molecular objects of course, other object types will appear in the default color (white). Mode 2 is object color. It applies to all object types. I learned that the "C > by element > ..." menu options also update the object color with the same color that is applied to carbons. A neat way to transfer atom color to object color is with this command: iterate (name CA), cmd.set_object_color(model, color) Other selections are possible of course. Cheers, Thomas > On Oct 2, 2019, at 7:31 PM, Jared Sampson wrote: > > Hi Thomas - > >> When I said it's easy to implement, I was only thinking of object color. >> Among the various cases you describe, the "dominant color" is probably the >> most important one, as it might not be obvious to the user that object color >> can be different from atom colors. > Indeed, I was among those for whom "it might not be obvious" that there are > separate object and atom colors! I had thought all coloring was done at the > atom level (as you show using the selection), and didn't realize there is a > separate object-level color, nor did I know about the `set_object_color` > command. > > Thanks for the explanation, Thomas! > > Cheers, > > Jared > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] feature request
Hi Thomas - When I said it's easy to implement, I was only thinking of object color. Among the various cases you describe, the "dominant color" is probably the most important one, as it might not be obvious to the user that object color can be different from atom colors. Indeed, I was among those for whom "it might not be obvious" that there are separate object and atom colors! I had thought all coloring was done at the atom level (as you show using the selection), and didn't realize there is a separate object-level color, nor did I know about the `set_object_color` command. Thanks for the explanation, Thomas! Cheers, Jared___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] feature request
Hi Jared and Vaheh -
Jared, you've put way more thought into this than I did :-) When I said it's
easy to implement, I was only thinking of object color. Among the various cases
you describe, the "dominant color" is probably the most important one, as it
might not be obvious to the user that object color can be different from atom
colors.
color blue, (obj);# only changes atom colors
color blue, obj ;# changes object and atom colors
cmd.set_object_color("obj", "blue") ;# only changes object color
More complex situations like spectrum or per-representation colors can be
neglected I think - I wouldn't know how to map those to a label color in a
useful way.
As a first step, I can add internal_gui_name_color_mode=1 with object colors.
Cheers,
Thomas
> On Oct 1, 2019, at 9:31 PM, Oganesyan, Vaheh
> wrote:
>
> Thomas and Jared,
> I’m not sure what will be the best solution, but as a start, color of the
> object name may stay white if more than one color is used. Because you both
> found this as an interesting idea allows me to ask similar question now
> regarding labels. What if we can get label_color match the residue color. I
> vaguely remember something like this discussed x number of years ago, but do
> not remember why not. Could label become property of the object and not just
> a property of a session?
>
> Thank you.
>
>
> From: Jared Sampson
> Sent: Tuesday, October 1, 2019 2:45 PM
> To: Oganesyan, Vaheh ; Thomas Holder
>
> Cc: pymol-users
> Subject: Re: [PyMOL] feature request
>
> Hi Thomas and Vaheh -
>
> This is indeed an interesting idea. I was thinking about this in terms of
> implementation, and what the edge cases might be. I wonder what would be the
> mechanism for assigning the color if the object is not just a single color.
> Would it be the color that is the dominant color of the object over all
> (visible) representations?
>
> What about a spectrum-colored object? Would it be possible to color the
> object name according to the colors in the spectrum (like the "spectrum" and
> "rainbow" menu items already in the OpenGL menu)?
>
> And what if there are different coloring schemes for the different
> representations—would there be a hierarchy in terms of choosing , e.g.
> surface > cartoon > stick > line, etc.?
>
> I definitely like Thomas' idea of a global `internal_gui_name_color_mode`
> setting to turn the menu object name coloring on/off. (Perhaps different
> modes could correspond to different ways of choosing the displayed color.)
> It might also be useful to include object-level (or named-selection-level)
> settings to override the global setting and specify the color or spectrum
> directly, e.g.:
>
> set internal_gui_name_color, red, obj1
> set internal_gui_name_spectrum, rainbow, obj1
>
> Really interesting suggestion, Vaheh. Looking forward to seeing how it might
> work!
>
> Cheers,
> Jared
>
> On October 1, 2019 at 5:13:07 AM, Thomas Holder
> (thomas.hol...@schrodinger.com) wrote:
>
> Hi Vaheh,
>
> I see that this can be useful, and it's fairly easy to implement. We can add
> a new setting to turn this on and off, like "internal_gui_name_color_mode"
> (or do you have a suggestion for a better name?).
>
> Cheers,
> Thomas
>
>
> > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh
> > wrote:
> >
> > Thomas and other PyMOL developers,
> >
> > It looks as if we color the object name similar to the object color it will
> > be easier to distinguish which structure am I manipulating now. While
> > models can be colored, the names of the models can't.
> > Anybody else think it might be helpful?
> >
> > Thank you.
> > Regards,
> >
> > Vaheh Oganesyan, Ph.D.
> > Scientist, Biologic Therapeutics
> >
> > AstraZeneca
> > R&D | Antibody Discovery and Protein Engineering
> > One Medimmune Way, Gaithersburg, MD 20878
> > T: 301-398-4640 M: 240-398-0046
> > vaheh.oganes...@astrazeneca.com
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
>
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Re: [PyMOL] feature request
Hi Vaheh -
Fortunately, `label_color` is an atom-level setting already. For example:
```
PyMOL>fab A, ala_pep
PyMOL>label n. CA, f"{resn} {resi}"
Label: labelled 5 atoms.
PyMOL>color white
Executive: Colored 50 atoms.
PyMOL>set label_color, red, resi 1
Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, orange, resi 2
Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, yellow, resi 3
Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, green, resi 4
Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, blue, resi 5
Setting: label_color set for 10 atoms in object "pep1".
```
Hope that helps.
Cheers,
Jared
On October 1, 2019 at 3:31:54 PM, Oganesyan, Vaheh
(vaheh.oganes...@astrazeneca.com) wrote:
Thomas and Jared,
I’m not sure what will be the best solution, but as a start, color of the
object name may stay white if more than one color is used. Because you both
found this as an interesting idea allows me to ask similar question now
regarding labels. What if we can get label_color match the residue color. I
vaguely remember something like this discussed x number of years ago, but do
not remember why not. Could label become property of the object and not just a
property of a session?
Thank you.
From: Jared Sampson
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh ; Thomas Holder
Cc: pymol-users
Subject: Re: [PyMOL] feature request
Hi Thomas and Vaheh -
This is indeed an interesting idea. I was thinking about this in terms of
implementation, and what the edge cases might be. I wonder what would be the
mechanism for assigning the color if the object is not just a single color.
Would it be the color that is the dominant color of the object over all
(visible) representations?
What about a spectrum-colored object? Would it be possible to color the object
name according to the colors in the spectrum (like the "spectrum" and "rainbow"
menu items already in the OpenGL menu)?
And what if there are different coloring schemes for the different
representations—would there be a hierarchy in terms of choosing , e.g. surface
> cartoon > stick > line, etc.?
I definitely like Thomas' idea of a global `internal_gui_name_color_mode`
setting to turn the menu object name coloring on/off. (Perhaps different modes
could correspond to different ways of choosing the displayed color.) It might
also be useful to include object-level (or named-selection-level) settings to
override the global setting and specify the color or spectrum directly, e.g.:
set internal_gui_name_color, red, obj1
set internal_gui_name_spectrum, rainbow, obj1
Really interesting suggestion, Vaheh. Looking forward to seeing how it might
work!
Cheers,
Jared
On October 1, 2019 at 5:13:07 AM, Thomas Holder (thomas.hol...@schrodinger.com)
wrote:
Hi Vaheh,
I see that this can be useful, and it's fairly easy to implement. We can add a
new setting to turn this on and off, like "internal_gui_name_color_mode" (or do
you have a suggestion for a better name?).
Cheers,
Thomas
> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh
> wrote:
>
> Thomas and other PyMOL developers,
>
> It looks as if we color the object name similar to the object color it will
> be easier to distinguish which structure am I manipulating now. While models
> can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>
> Thank you.
> Regards,
>
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
>
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046
> vaheh.oganes...@astrazeneca.com
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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Re: [PyMOL] feature request
Thomas and Jared, I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session? Thank you. From: Jared Sampson Sent: Tuesday, October 1, 2019 2:45 PM To: Oganesyan, Vaheh ; Thomas Holder Cc: pymol-users Subject: Re: [PyMOL] feature request Hi Thomas and Vaheh - This is indeed an interesting idea. I was thinking about this in terms of implementation, and what the edge cases might be. I wonder what would be the mechanism for assigning the color if the object is not just a single color. Would it be the color that is the dominant color of the object over all (visible) representations? What about a spectrum-colored object? Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)? And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.? I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off. (Perhaps different modes could correspond to different ways of choosing the displayed color.) It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.: set internal_gui_name_color, red, obj1 set internal_gui_name_spectrum, rainbow, obj1 Really interesting suggestion, Vaheh. Looking forward to seeing how it might work! Cheers, Jared On October 1, 2019 at 5:13:07 AM, Thomas Holder (thomas.hol...@schrodinger.com<mailto:thomas.hol...@schrodinger.com>) wrote: Hi Vaheh, I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?). Cheers, Thomas > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh > mailto:vaheh.oganes...@astrazeneca.com>> > wrote: > > Thomas and other PyMOL developers, > > It looks as if we color the object name similar to the object color it will > be easier to distinguish which structure am I manipulating now. While models > can be colored, the names of the models can't. > Anybody else think it might be helpful? > > Thank you. > Regards, > > Vaheh Oganesyan, Ph.D. > Scientist, Biologic Therapeutics > > AstraZeneca > R&D | Antibody Discovery and Protein Engineering > One Medimmune Way, Gaithersburg, MD 20878 > T: 301-398-4640 M: 240-398-0046 > vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com> -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: https://clicktime.symantec.com/3UV6BFZxvbLGNd6ZnGajdMx6H2?u=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net Unsubscribe: https://clicktime.symantec.com/3E9dosvp4WJ7Ck38g9VwWNV6H2?u=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] feature request
Hi Thomas and Vaheh - This is indeed an interesting idea. I was thinking about this in terms of implementation, and what the edge cases might be. I wonder what would be the mechanism for assigning the color if the object is not just a single color. Would it be the color that is the dominant color of the object over all (visible) representations? What about a spectrum-colored object? Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)? And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.? I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off. (Perhaps different modes could correspond to different ways of choosing the displayed color.) It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.: set internal_gui_name_color, red, obj1 set internal_gui_name_spectrum, rainbow, obj1 Really interesting suggestion, Vaheh. Looking forward to seeing how it might work! Cheers, Jared On October 1, 2019 at 5:13:07 AM, Thomas Holder (thomas.hol...@schrodinger.com) wrote: Hi Vaheh, I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?). Cheers, Thomas > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh > wrote: > > Thomas and other PyMOL developers, > > It looks as if we color the object name similar to the object color it will > be easier to distinguish which structure am I manipulating now. While models > can be colored, the names of the models can't. > Anybody else think it might be helpful? > > Thank you. > Regards, > > Vaheh Oganesyan, Ph.D. > Scientist, Biologic Therapeutics > > AstraZeneca > R&D | Antibody Discovery and Protein Engineering > One Medimmune Way, Gaithersburg, MD 20878 > T: 301-398-4640 M: 240-398-0046 > vaheh.oganes...@astrazeneca.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] feature request
Hi Vaheh, I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?). Cheers, Thomas > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh > wrote: > > Thomas and other PyMOL developers, > > It looks as if we color the object name similar to the object color it will > be easier to distinguish which structure am I manipulating now. While models > can be colored, the names of the models can't. > Anybody else think it might be helpful? > > Thank you. > Regards, > > Vaheh Oganesyan, Ph.D. > Scientist, Biologic Therapeutics > > AstraZeneca > R&D | Antibody Discovery and Protein Engineering > One Medimmune Way, Gaithersburg, MD 20878 > T: 301-398-4640 M: 240-398-0046 > vaheh.oganes...@astrazeneca.com -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] feature request
Thomas and other PyMOL developers, It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't. Anybody else think it might be helpful? Thank you. Regards, Vaheh Oganesyan, Ph.D. Scientist, Biologic Therapeutics AstraZeneca R&D | Antibody Discovery and Protein Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-4640 M: 240-398-0046 vaheh.oganes...@astrazeneca.com ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] feature request: supercell construction
Hi Nick, > I noticed a few things: > > - when I run "supercell 2, 1, 1" I get another cell outline along the > a axis, but no atoms are shown in the second cell. Do I have to run > another command for them to show up? the script does not create symmetry mates. The "symexp" command can create symmetry mates within a given radius (it will not just fill up the cell). > - when I run the command again with other values for a, b, or c, > nothing changes. I would expect that running the sequence "supercell > 2, 1, 1" and then "supercell 2, 2, 1" would show me a 2x2x1 supercell > at the end, but I see only the 2x1x1 supercell. the second call will create a new state for the same object. This is not convenient, so I changed it to replace the first state again. I put the modified script to the PyMOLWiki: http://www.pymolwiki.org/index.php/Supercell Cheers, Thomas -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request: supercell construction
Hi Thomas, thanks! I noticed a few things: - when I run "supercell 2, 1, 1" I get another cell outline along the a axis, but no atoms are shown in the second cell. Do I have to run another command for them to show up? - when I run the command again with other values for a, b, or c, nothing changes. I would expect that running the sequence "supercell 2, 1, 1" and then "supercell 2, 2, 1" would show me a 2x2x1 supercell at the end, but I see only the 2x1x1 supercell. Thanks again, nick On Wed, Apr 14, 2010 at 03:24, Thomas Holder wrote: > Hi Nick, > > I recently was playing with (aka learning) the crystallographic symmetry > information in PDB files and now took your feature request as an > exercise. See attached file, hope it does what you had in mind. > > Cheers, > Thomas > > On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote: > > It would be great if pymol had support for constructing and displaying > > a supercell: > > > > For data files that support crystallographic information, e.g. pdb, > > pymol can already display the unit cell (show cell). It would be great > > if one could easily display multiple copies of the unit cell, along > > the lines of > > > > supercell 1,1,2 > > > > where pymol would then copy the unit cell along the c-axis and display > > 2 unit cells. > > > > supercell 2,2,2 > > > > would display 2 copies along the a, b, and c axes, and display 8 unit > > cells in total. > > > > As a related request it would be great if pymol could construct a unit > > cell in case the crystallographic information in the input file does > > not exist. This could come in handy for instance when reading from > > xyz. Maybe a command such as > > > > construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90, > > gamma=90 > > > > would construct a cubic cell with dimensions axbxc. > > > > Thanks, > > > > nick > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request: supercell construction
Hi Nick,
I recently was playing with (aka learning) the crystallographic symmetry
information in PDB files and now took your feature request as an
exercise. See attached file, hope it does what you had in mind.
Cheers,
Thomas
On Mon, 2010-04-12 at 14:12 -0600, Nicolas Bock wrote:
> It would be great if pymol had support for constructing and displaying
> a supercell:
>
> For data files that support crystallographic information, e.g. pdb,
> pymol can already display the unit cell (show cell). It would be great
> if one could easily display multiple copies of the unit cell, along
> the lines of
>
> supercell 1,1,2
>
> where pymol would then copy the unit cell along the c-axis and display
> 2 unit cells.
>
> supercell 2,2,2
>
> would display 2 copies along the a, b, and c axes, and display 8 unit
> cells in total.
>
> As a related request it would be great if pymol could construct a unit
> cell in case the crystallographic information in the input file does
> not exist. This could come in handy for instance when reading from
> xyz. Maybe a command such as
>
> construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90,
> gamma=90
>
> would construct a cubic cell with dimensions axbxc.
>
> Thanks,
>
> nick
'''
(c) 2010 Thomas Holder
PyMOL python script (load with `run supercell.py`)
Usage: See "help supercell"
'''
from pymol import cmd, cgo
from math import cos, sin, radians, sqrt
import numpy
def cellbasis(angles, edges):
'''
For the unit cell with given angles and edge lengths calculate the basis
transformation (vectors) as a 4x4 numpy.array
'''
rad = [radians(i) for i in angles]
basis = numpy.identity(4)
basis[0][1] = cos(rad[2])
basis[1][1] = sin(rad[2])
basis[0][2] = cos(rad[1])
basis[1][2] = (cos(rad[0]) - basis[0][1]*basis[0][2])/basis[1][1]
basis[2][2] = sqrt(1 - basis[0][2]**2 - basis[1][2]**2)
edges.append(1.0)
return basis * edges # numpy.array multiplication!
def supercell(a=1, b=1, c=1, object=None, color='blue'):
'''
DESCRIPTION
Draw a supercell, as requested by Nicolas Bock on the pymol-users
mailing list (Subject: [PyMOL] feature request: supercell construction
Date: 04/12/2010 10:12:17 PM (Mon, 12 Apr 2010 14:12:17 -0600))
USAGE
supercell a, b, c [, object [, color]]
ARGUMENTS
a, b, c = integer: repeat cell in x,y,z direction a,b,c times
{default: 1,1,1}
object = string: name of object to take cell definition from
color = string: color of cell {default: blue}
SEE ALSO
show cell
'''
if object is None:
object = cmd.get_object_list()[0]
sym = cmd.get_symmetry(object)
cell_edges = sym[0:3]
cell_angles = sym[3:6]
basis = cellbasis(cell_angles, cell_edges)
assert isinstance(basis, numpy.ndarray)
ts = list()
for i in range(int(a)):
for j in range(int(b)):
for k in range(int(c)):
ts.append([i,j,k])
obj = [
cgo.BEGIN,
cgo.LINES,
cgo.COLOR,
]
obj.extend(cmd.get_color_tuple(color))
for t in ts:
shift = basis[0:3,0:3] * t
shift = shift[:,0] + shift[:,1] + shift[:,2]
for i in range(3):
vi = basis[0:3,i]
vj = [
numpy.array([0.,0.,0.]),
basis[0:3,(i+1)%3],
basis[0:3,(i+2)%3],
basis[0:3,(i+1)%3] + basis[0:3,(i+2)%3]
]
for j in range(4):
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j]).tolist())
obj.append(cgo.VERTEX)
obj.extend((shift + vj[j] + vi).tolist())
cmd.load_cgo(obj, 'supercell')
cmd.extend('supercell', supercell)
--
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[PyMOL] feature request: supercell construction
It would be great if pymol had support for constructing and displaying a supercell: For data files that support crystallographic information, e.g. pdb, pymol can already display the unit cell (show cell). It would be great if one could easily display multiple copies of the unit cell, along the lines of supercell 1,1,2 where pymol would then copy the unit cell along the c-axis and display 2 unit cells. supercell 2,2,2 would display 2 copies along the a, b, and c axes, and display 8 unit cells in total. As a related request it would be great if pymol could construct a unit cell in case the crystallographic information in the input file does not exist. This could come in handy for instance when reading from xyz. Maybe a command such as construct_supercell a=10.2, b=10.2, c=15, alpha=90.0, beta=90, gamma=90 would construct a cubic cell with dimensions axbxc. Thanks, nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
Could the connect_mode setting be better documented? The current documentation doesn't say much about what that setting does. nick On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
Great, that works! On Fri, Mar 12, 2010 at 12:08, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Nicolas, > > Try: > > set connect_mode, 2 > load yourXYZ.xyz, discrete=1 > > -- Jason > > On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock > wrote: > > Please find attached an example xyz file. > > > > nick > > > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock > wrote: > >> > >> When I load an xyz file with several frames (for example the result of > an > >> MD simulation) I find that pymol calculates and sets the bonds only > using > >> the initial frame. For frames > 1 the bonds are not recalculated. The > only > >> "work around" I found is to load(..., multiplex=1) which loads the > frames > >> into separate objects. But now I can not play the MD trajectory as a > movie. > >> > >> I would like to suggest that this feature be added to pymol so that MD > >> trajectories can be played with proper bonding for all frames. > >> > >> Thanks > >> > >> nick > >> > > > > > > > -- > > Download Intel® Parallel Studio Eval > > Try the new software tools for yourself. Speed compiling, find bugs > > proactively, and fine-tune applications for parallel performance. > > See why Intel Parallel Studio got high marks during beta. > > http://p.sf.net/sfu/intel-sw-dev > > ___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
Nicolas, Try: set connect_mode, 2 load yourXYZ.xyz, discrete=1 -- Jason On Fri, Mar 12, 2010 at 1:50 PM, Nicolas Bock wrote: > Please find attached an example xyz file. > > nick > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: >> >> When I load an xyz file with several frames (for example the result of an >> MD simulation) I find that pymol calculates and sets the bonds only using >> the initial frame. For frames > 1 the bonds are not recalculated. The only >> "work around" I found is to load(..., multiplex=1) which loads the frames >> into separate objects. But now I can not play the MD trajectory as a movie. >> >> I would like to suggest that this feature be added to pymol so that MD >> trajectories can be played with proper bonding for all frames. >> >> Thanks >> >> nick >> > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
I should mention that the first 3 columns are the cartesian coordinates in Angstroms, and the last 3 columes the forces in eV/A. On Fri, Mar 12, 2010 at 11:50, Nicolas Bock wrote: > Please find attached an example xyz file. > > nick > > > > On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > >> When I load an xyz file with several frames (for example the result of an >> MD simulation) I find that pymol calculates and sets the bonds only using >> the initial frame. For frames > 1 the bonds are not recalculated. The only >> "work around" I found is to load(..., multiplex=1) which loads the frames >> into separate objects. But now I can not play the MD trajectory as a movie. >> >> I would like to suggest that this feature be added to pymol so that MD >> trajectories can be played with proper bonding for all frames. >> >> Thanks >> >> nick >> >> > -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
Please find attached an example xyz file. nick On Fri, Mar 12, 2010 at 11:20, Nicolas Bock wrote: > When I load an xyz file with several frames (for example the result of an > MD simulation) I find that pymol calculates and sets the bonds only using > the initial frame. For frames > 1 the bonds are not recalculated. The only > "work around" I found is to load(..., multiplex=1) which loads the frames > into separate objects. But now I can not play the MD trajectory as a movie. > > I would like to suggest that this feature be added to pymol so that MD > trajectories can be played with proper bonding for all frames. > > Thanks > > nick > > HCN_to_CHN.xyz Description: Protein Databank data -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] feature request
After editing a molecule it can happen that the bonds that used to be there don't all make sense anymore, for example, because I moved an atom pretty far away from its original place. It would be nice if one could call a function to force pymol at some point to recalculate the bonds in the molecule. Unfortunately there is currently no "rebond" function. I would like to suggest that it be added. Thanks nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] feature request
When I load an xyz file with several frames (for example the result of an MD simulation) I find that pymol calculates and sets the bonds only using the initial frame. For frames > 1 the bonds are not recalculated. The only "work around" I found is to load(..., multiplex=1) which loads the frames into separate objects. But now I can not play the MD trajectory as a movie. I would like to suggest that this feature be added to pymol so that MD trajectories can be played with proper bonding for all frames. Thanks nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request?
Nick, Please email bug reports and feature suggestions to h...@schrodinger.com. CC the list if you like. Cheers, -- Jason On Fri, Mar 12, 2010 at 11:17 AM, Nicolas Bock wrote: > Hello list, > > what's the mechanism for submitting feature requests or bug reports? To this > list? > > nick > > > -- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] feature request?
Hello list, what's the mechanism for submitting feature requests or bug reports? To this list? nick -- Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Feature Request/Ideas
Hi, I would definitely not like to see a default representation to be any more than lines (as it is now). Opening one of my 100,000 atom MD trajectory frames would take far longer than it's worth. Regarding png output, I think this is in there already (but don't remember) - I'd like to be able to specify one dimension (usually width) and have the other automatically calculated. If I'm trying to frame a molecule and adjust the size of the screen window I'll want output to keep the same aspect ratio. Also, I see a major slowdown when running remotely as compared to VMD, especially with regards to using the menus (top and right). I get an "unable to create direct context rendering" message, and while I don't expect it to perform as well as when running locally, I get very adequate performance running VMD over the same connection. This is useful when checking of MD or NMR calculations on a remote cluster from my lab machines. The slowdown (especially the view descriptor menu on the right side) is apparent even over a gigE lan. I'll add another voice for a better undo function. In my specific case I can think of a number of times where I've highlighted a collection of residues as spheres and then accidentally added spheres to the whole molecule instead of the next selection. Being able to get back from that (even one step) would be a time-saver. Dave - David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm -Original Message- From: David Hall [mailto:dwash59_2...@yahoo.com] Sent: Thursday, January 21, 2010 9:20 AM To: Jason Vertrees; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] PyMOL on the Mac Alright, here's a feature request that might convince people who still don't believe, despite your first commit to pymol trunk post-acquisition including "Fixed a GL build bug on OSX" (see http://pymol.svn.sourceforge.net/viewvc/pymol?view=rev&revision=3887 ) A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Hopefully I'm out of ideas nows, David -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] feature request
Adam, What you seek is in the 1.2 beta -- enable "buttons" from the Scene menu or: set scene_buttons You can then drag to reorder within the stack, rename, update, and delete -- all with the right mouse button. Left-click takes you to the scene you click on, and middle-click-and-drag allows you to sweep through all of the scenes present, just like with residues in the sequence viewer or objects within the object stack. What I believe Sarina is referring to is the fact that only the name is shown in the Scene Button stack, not an actual thumb of the image. That would make Scene Buttons more like PowerPoint's slide sorter pane, rather than merely table of names or numbers. Cheers, Warren PS. We haven't made much noise about 1.2 beta yet because there are still enough known glitches with the new features for users to be wary. We'll certainly let everyone know when it make sense for more people to try it! -Original Message- From: H. Adam Steinberg [mailto:a...@steinbergs.us] Sent: Fri 1/16/2009 6:41 PM To: Sarina Bromberg Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] feature request It is especially difficult to remember which scene is which when you open a pse file that you haven't looked at for a few months. Would it be simple or easy to just let us name the scenes like we name the objects and selections in the pane on the right? Sarina Bromberg wrote: > I find it difficult to keep track of all the scenes I create in a > PyMOL session and where they are in the stack. Would it be possible, > at some point, to add a feature that displays numbered thumbnails of > scenes in another window on the desktop? > Thanks, > Sarina > Sarina Bromberg > (650) 879-1492 > PO Box 12, Pescadero, CA 94060 > sarina.bromb...@att.net > > > > > > > -- > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] feature request
It is especially difficult to remember which scene is which when you open a pse file that you haven't looked at for a few months. Would it be simple or easy to just let us name the scenes like we name the objects and selections in the pane on the right? Sarina Bromberg wrote: I find it difficult to keep track of all the scenes I create in a PyMOL session and where they are in the stack. Would it be possible, at some point, to add a feature that displays numbered thumbnails of scenes in another window on the desktop? Thanks, Sarina Sarina Bromberg (650) 879-1492 PO Box 12, Pescadero, CA 94060 sarina.bromb...@att.net -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
[PyMOL] feature request
I find it difficult to keep track of all the scenes I create in a PyMOL session and where they are in the stack. Would it be possible, at some point, to add a feature that displays numbered thumbnails of scenes in another window on the desktop? Thanks, Sarina Sarina Bromberg (650) 879-1492 PO Box 12, Pescadero, CA 94060 sarina.bromb...@att.net
Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append("%-30s %s"%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title="Settings",
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry("500x400")
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append("%-30s %s"%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
> While we're discussing ways to make our favorite program a little
> better, I had an idea I thought I'd throw out there...
>
> While making some figures the other day, I found myself scrolling
> endlessly through the edit settings menu (under Setting --> Edit All) a
> number of times, mostly to locate a relatively small number of settings
> related to ray tracing. This got me thinking about a way to improve
> access to the many wonderful features that have been added to PyMOL.
>
> The solution I came up with is a filter line which could be placed
> directly above the window listing all the settings. Users could then
> type a word, say "ray" or "cartoon", and only the settings containing
> this word would be shown.
>
> The best example of a program containing this feature is the
> "about:config" window in Firefox. When you open a browser and type
> "about:config" instead of an address, a window containing hundreds of
> settings appears. At the top is a filter bar which you can use to pare
> down the number of settings listed below.
>
> I think this would be a great addition to PyMOL and would help users
> familiarize themselves with the many new settings which have been (and
> will be) implemented. :)
>
> Perhaps others have even better solutions to this problem. The use of a
> filter is just the first idea which came to my mind. I think it would be
> relatively easy to implement, although my python programming skills are
> somewhat limited.
>
> Thanks,
> Michelle Gill
>
>
> ---
> This SF.Net email is sponsored by xPML, a groundbreaking scripting language
> that extends applications into web and mobile media. Attend the live
> webcast and join the prime developer group breaking into this new coding
> territory!
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Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hello Michelle,
You can also edit the SetEditor.py file. The file is in the
'/usr/lib/python2.3/site-packages/pmg_tk' directory on linux and add the
feature. It can be done by adding to small portion of add-on code to the
file. If you do so:
Keep a copy of the original file in a safe place !
Here is a part of the modified file:
###
class SetEditor:
def __init__(self,app):
self.app = app
self.list = []
for a in pymol.setting.get_index_list():
self.list.append("%-30s %s"%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.index = {}
c = 0
for a in pymol.setting.get_name_list():
self.index[a] = c
c = c + 1
self.dialog = Pmw.SelectionDialog(self.app.root,title="Settings",
buttons = ('Edit', 'Done'),
defaultbutton='Edit',
scrolledlist_labelpos=N,
label_text='Double click to edit',
scrolledlist_items = self.list,
command = self.command)
self.dialog.geometry("500x400")
# start of the add-on
interior = self.dialog.interior()
self.filter = Pmw.EntryField(interior,
labelpos = 'w',
label_text= 'Filter:',
validate = None,
command = self.filter_list)
self.filter.pack()
# end of the add-on
self.listbox = self.dialog.component('scrolledlist')
self.listbox.component('listbox').configure(font=app.my_fw_font)
self.dialog.protocol('WM_DELETE_WINDOW',self.cancel)
app.my_show(self.dialog)
# start of the add-on
def filter_list(self):
self.list = []
for a in pymol.setting.get_index_list():
if self.filter.getvalue() in pymol.setting._get_name(a):
self.list.append("%-30s %s"%(pymol.setting._get_name(a),
cmd.get_setting_text(a,'',-1)))
self.dialog.setlist(self.list)
self.dialog.update()
# end of the add-on
def cancel(self,event=None):
self.command(result='Done')
###
This code works fine on my linux box. If you have some problem, don't hesitate
to ask me !
Cheers,
Jerome Pansanel
Le Mardi 18 Avril 2006 18:02, Michelle Gill a écrit :
> While we're discussing ways to make our favorite program a little
> better, I had an idea I thought I'd throw out there...
>
> While making some figures the other day, I found myself scrolling
> endlessly through the edit settings menu (under Setting --> Edit All) a
> number of times, mostly to locate a relatively small number of settings
> related to ray tracing. This got me thinking about a way to improve
> access to the many wonderful features that have been added to PyMOL.
>
> The solution I came up with is a filter line which could be placed
> directly above the window listing all the settings. Users could then
> type a word, say "ray" or "cartoon", and only the settings containing
> this word would be shown.
>
> The best example of a program containing this feature is the
> "about:config" window in Firefox. When you open a browser and type
> "about:config" instead of an address, a window containing hundreds of
> settings appears. At the top is a filter bar which you can use to pare
> down the number of settings listed below.
>
> I think this would be a great addition to PyMOL and would help users
> familiarize themselves with the many new settings which have been (and
> will be) implemented. :)
>
> Perhaps others have even better solutions to this problem. The use of a
> filter is just the first idea which came to my mind. I think it would be
> relatively easy to implement, although my python programming skills are
> somewhat limited.
>
> Thanks,
> Michelle Gill
>
>
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Re: [PyMOL] (small) Pymol feature request--filter for edit settings window
Hey Michelle, Ezequiel Panepucci wrote grepset, a little script that allows you to do exactly what you want and even more. No need even to open the edit settings menu, just type 'grepset ray', and you're cruising. Get grepset from http://www.pymolwiki.org/index.php/Grepset and put it into your .pymolrc file as 'run /path/to/grepset.py'. Life is good. Andreas Michelle Gill wrote: While we're discussing ways to make our favorite program a little better, I had an idea I thought I'd throw out there... While making some figures the other day, I found myself scrolling endlessly through the edit settings menu (under Setting --> Edit All) a number of times, mostly to locate a relatively small number of settings related to ray tracing. This got me thinking about a way to improve access to the many wonderful features that have been added to PyMOL. The solution I came up with is a filter line which could be placed directly above the window listing all the settings. Users could then type a word, say "ray" or "cartoon", and only the settings containing this word would be shown. The best example of a program containing this feature is the "about:config" window in Firefox. When you open a browser and type "about:config" instead of an address, a window containing hundreds of settings appears. At the top is a filter bar which you can use to pare down the number of settings listed below. I think this would be a great addition to PyMOL and would help users familiarize themselves with the many new settings which have been (and will be) implemented. :) Perhaps others have even better solutions to this problem. The use of a filter is just the first idea which came to my mind. I think it would be relatively easy to implement, although my python programming skills are somewhat limited. Thanks, Michelle Gill -- --> Andreas Förster <-- 8 rue Doudart de Lagrée, 38000 Grenoble ++33.(0)438.866201 and ++33.(0)456.452000 www.biochem.utah.edu/~andreas docandreas.blogspot.com
[PyMOL] (small) Pymol feature request--filter for edit settings window
While we're discussing ways to make our favorite program a little better, I had an idea I thought I'd throw out there... While making some figures the other day, I found myself scrolling endlessly through the edit settings menu (under Setting --> Edit All) a number of times, mostly to locate a relatively small number of settings related to ray tracing. This got me thinking about a way to improve access to the many wonderful features that have been added to PyMOL. The solution I came up with is a filter line which could be placed directly above the window listing all the settings. Users could then type a word, say "ray" or "cartoon", and only the settings containing this word would be shown. The best example of a program containing this feature is the "about:config" window in Firefox. When you open a browser and type "about:config" instead of an address, a window containing hundreds of settings appears. At the top is a filter bar which you can use to pare down the number of settings listed below. I think this would be a great addition to PyMOL and would help users familiarize themselves with the many new settings which have been (and will be) implemented. :) Perhaps others have even better solutions to this problem. The use of a filter is just the first idea which came to my mind. I think it would be relatively easy to implement, although my python programming skills are somewhat limited. Thanks, Michelle Gill
