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From: Ramiro T. S. <urc...@gm...> - 2011-04-06 09:23:00
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Hi and thanks for reading this. I have googled for a way to achieve what I want and have gone through the wiki, to no avail. I would like to color in a different way the different helix types: alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get distinct colors for each type by default. But if the same pdb file is open with PyMOL all helices are treated the same way. Can't PyMOL distinguish helix types? Thanks in advance, Ramiro Téllez Sanz Dept. Physical Chemistry University of Almeria Spain |
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From: Jason V. <jas...@sc...> - 2011-04-06 13:17:22
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Hi Ramiro, PyMOL doesn't differentiate helices, so it cannot color them differently. If you had the residue labels from some other program you could read them in and then color by type. Cheers, -- Jason On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urc...@gm...> wrote: > Hi and thanks for reading this. > > I have googled for a way to achieve what I want and have gone through > the wiki, to no avail. > > I would like to color in a different way the different helix types: > alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get > distinct colors for each type by default. But if the same pdb file is > open with PyMOL all helices are treated the same way. Can't PyMOL > distinguish helix types? > > Thanks in advance, > Ramiro Téllez Sanz > Dept. Physical Chemistry > University of Almeria > Spain > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > 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 |
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From: H. A. S. <ad...@st...> - 2011-04-06 14:47:59
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Hi Ramiro, Like you, I would love to see secondary structure colored by helix type. Jmol however does not show this as a default. Do you know what steps you took to get Jmol to show secondary structure colored by helix type? I can't seem to find that setting in any of the menu options. style/scheme/cartoon color/structure/cartoon/By Scheme/Secondary Structure This shows all of the helices in the same color. Adam On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote: > Hi and thanks for reading this. > > I have googled for a way to achieve what I want and have gone through > the wiki, to no avail. > > I would like to color in a different way the different helix types: > alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get > distinct colors for each type by default. But if the same pdb file is > open with PyMOL all helices are treated the same way. Can't PyMOL > distinguish helix types? > > Thanks in advance, > Ramiro Téllez Sanz > Dept. Physical Chemistry > University of Almeria > Spain > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... artforscience H. Adam Steinberg Artist, Scientist, Developmental Editor www.artforscience.com 7904 Bowman Rd Lodi, WI 53555 608/729-5944 |
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From: Hongbo Z. <hon...@bi...> - 2011-04-12 14:22:08
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Hi, if anybody is still interested in the topic, I have made a DSSP plugin for running DSSP and coloring proteins according to the DSSP secondary structure assignment. Please have a look at: http://www.pymolwiki.org/index.php/DSSP This plugin invokes DSSP (presuming you already have DSSP binary on your hard drive) and reads the output using BioPython. It then makes several selections, each for a kind of secondary structure elements (SSE) if there is at least one residue in the input selection is assigned with the SSE. regards, hongbo On 04/06/2011 04:34 PM, H. Adam Steinberg wrote: > Hi Ramiro, > > Like you, I would love to see secondary structure colored by helix type. > Jmol however does not show this as a default. Do you know what steps you > took to get Jmol to show secondary structure colored by helix type? > > I can't seem to find that setting in any of the menu options. > > style/scheme/cartoon > color/structure/cartoon/By Scheme/Secondary Structure > > This shows all of the helices in the same color. > > Adam > > > On Apr 6, 2011, at 4:22 AM, Ramiro Téllez Sanz wrote: > >> Hi and thanks for reading this. >> >> I have googled for a way to achieve what I want and have gone through >> the wiki, to no avail. >> >> I would like to color in a different way the different helix types: >> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get >> distinct colors for each type by default. But if the same pdb file is >> open with PyMOL all helices are treated the same way. Can't PyMOL >> distinguish helix types? >> >> Thanks in advance, >> Ramiro Téllez Sanz >> Dept. Physical Chemistry >> University of Almeria >> Spain >> >> ------------------------------------------------------------------------------ >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizon-sfdev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > * > *art*/for/*science* > > *H. Adam Steinberg* > Artist, Scientist, Developmental Editor > > www.artforscience.com <http://www.artforscience.com> > 7904 Bowman Rd > Lodi, WI 53555 > 608/729-5944 > > * > > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > > > > _______________________________________________ > 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: Jason V. <jas...@sc...> - 2011-04-12 15:15:45
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Hi Hongbo, > Hi, if anybody is still interested in the topic, I have made a DSSP > plugin for running DSSP and coloring proteins according to the DSSP > secondary structure assignment. Please have a look at: > > http://www.pymolwiki.org/index.php/DSSP Very nice. Thanks for making and distributing this. I like the idea of people citing plugins. It could help readers find the plugin for their own use. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Thomas H. <sp...@us...> - 2011-04-12 15:42:11
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Hi Hongbo, very nice! Your plugin only accepts named selections, predefined selections like (all), (polymer) or object names do not work. Could you change this? Cheers, Thomas On Tue, Apr 12, 2011 at 4:22 PM, Hongbo Zhu <hon...@bi...> wrote: > Hi, if anybody is still interested in the topic, I have made a DSSP > plugin for running DSSP and coloring proteins according to the DSSP > secondary structure assignment. Please have a look at: > > http://www.pymolwiki.org/index.php/DSSP > > This plugin invokes DSSP (presuming you already have DSSP binary on your > hard drive) and reads the output using BioPython. It then makes several > selections, each for a kind of secondary structure elements (SSE) if > there is at least one residue in the input selection is assigned with > the SSE. > > regards, > hongbo -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
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From: Hongbo Z. <hon...@bi...> - 2011-04-13 07:12:24
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Hi, Jason and Thomas,
Thank you for your interest and suggestions!
The plugin has been updated s.t. it now also recognizes objects. The
support for single-word selectors ('polymer', 'all', etc) is also added.
Thanks again for the feedback!
best regards,
hongbo
On 04/12/2011 05:16 PM, Thomas Holder wrote:
> Hi Hongbo,
>
> very nice!
>
> Your plugin only accepts named selections, predefined selections like
> (all), (polymer) or object names do not work. Could you change this?
>
> Cheers,
> Thomas
>
> On Tue, Apr 12, 2011 at 4:22 PM, Hongbo Zhu
> <hon...@bi...> wrote:
>> Hi, if anybody is still interested in the topic, I have made a DSSP
>> plugin for running DSSP and coloring proteins according to the DSSP
>> secondary structure assignment. Please have a look at:
>>
>> http://www.pymolwiki.org/index.php/DSSP
>>
>> This plugin invokes DSSP (presuming you already have DSSP binary on your
>> hard drive) and reads the output using BioPython. It then makes several
>> selections, each for a kind of secondary structure elements (SSE) if
>> there is at least one residue in the input selection is assigned with
>> the SSE.
>>
>> regards,
>> hongbo
>
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From: Hongbo Z. <hon...@bi...> - 2011-04-25 00:13:11
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Hi, just for your information, the "DSSP plugin for PyMOL" has been updated to "DSSP & Stride plugin for PyMOL" :-) The plugin generates a selection for each SSE type assigned by DSSP or Stride. Using the brilliant "copy to object" function of PyMOL, you can make two copies of protein fragments of the same SSE defined by DSSP and Stride respectively and compare them visually ! The plugin also accepts (correct) PyMOL selection expressions as input beside selection/object names. Thanks for Thomas Holder for the suggestion! Your feedback and suggestions are always welcome! cheers,hongbo On 04/12/2011 04:22 PM, Hongbo Zhu wrote: > Hi, if anybody is still interested in the topic, I have made a DSSP > plugin for running DSSP and coloring proteins according to the DSSP > secondary structure assignment. Please have a look at: > > http://www.pymolwiki.org/index.php/DSSP > > This plugin invokes DSSP (presuming you already have DSSP binary on your > hard drive) and reads the output using BioPython. It then makes several > selections, each for a kind of secondary structure elements (SSE) if > there is at least one residue in the input selection is assigned with > the SSE. > > regards, > hongbo > > On 04/06/2011 04:34 PM, H. Adam Steinberg wrote: >> Hi Ramiro, >> >> Like you, I would love to see secondary structure colored by helix type. >> Jmol however does not show this as a default. Do you know what steps you >> took to get Jmol to show secondary structure colored by helix type? >> >> I can't seem to find that setting in any of the menu options. >> >> style/scheme/cartoon >> color/structure/cartoon/By Scheme/Secondary Structure >> >> This shows all of the helices in the same color. >> >> Adam >> -- Hongbo ZHU Postdoctoral Researcher Structural Bioinformatics Technische Universität Dresden Biotechnology Center Tatzberg 47/49 01307 Dresden, Germany Tel: +49 (0) 351 463-40083 Fax: +49 (0) 351 463-40087 E-Mail: hongbo.zhu at biotec Webpage: www.biotec.tu-dresden.de |
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From: H. A. S. <ad...@st...> - 2011-04-06 15:49:50
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Jason (or someone else), Is there way in pymol to look for the following angle in a structure φ=-49o and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to search for a few degrees plus of minus of those angles. They should all appear in tight turns and last for about 3 or 4 amino acids (I don't think there wouldn't be any cartoon helix shown). I don't think there are any pdbs yet that contain pi helices (because of the loose packing and steric hindrance of the side chains), does anyone know of any? Thanks Adam On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote: > Hi Ramiro, > > PyMOL doesn't differentiate helices, so it cannot color them > differently. If you had the residue labels from some other program > you could read them in and then color by type. > > Cheers, > > -- Jason > > On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urc...@gm...> wrote: >> Hi and thanks for reading this. >> >> I have googled for a way to achieve what I want and have gone through >> the wiki, to no avail. >> >> I would like to color in a different way the different helix types: >> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get >> distinct colors for each type by default. But if the same pdb file is >> open with PyMOL all helices are treated the same way. Can't PyMOL >> distinguish helix types? >> >> Thanks in advance, >> Ramiro Téllez Sanz >> Dept. Physical Chemistry >> University of Almeria >> Spain >> >> ------------------------------------------------------------------------------ >> Xperia(TM) PLAY >> It's a major breakthrough. An authentic gaming >> smartphone on the nation's most reliable network. >> And it wants your games. >> http://p.sf.net/sfu/verizon-sfdev >> _______________________________________________ >> 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 > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... artforscience H. Adam Steinberg Artist, Scientist, Developmental Editor www.artforscience.com 7904 Bowman Rd Lodi, WI 53555 608/729-5944 |
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From: Jason V. <jas...@sc...> - 2011-04-06 21:05:20
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Hi Adam, You could script this using the angle command with specific selections. Cheers, -- Jason On Wed, Apr 6, 2011 at 11:49 AM, H. Adam Steinberg <ad...@st...> wrote: > Jason (or someone else), > Is there way in pymol to look for the following angle in a structure φ=-49o > and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to > search for a few degrees plus of minus of those angles. They should all > appear in tight turns and last for about 3 or 4 amino acids (I don't think > there wouldn't be any cartoon helix shown). > I don't think there are any pdbs yet that contain pi helices (because of the > loose packing and steric hindrance of the side chains), does anyone know of > any? > Thanks > Adam > On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote: > > Hi Ramiro, > > PyMOL doesn't differentiate helices, so it cannot color them > differently. If you had the residue labels from some other program > you could read them in and then color by type. > > Cheers, > > -- Jason > > On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urc...@gm...> > wrote: > > Hi and thanks for reading this. > > I have googled for a way to achieve what I want and have gone through > > the wiki, to no avail. > > I would like to color in a different way the different helix types: > > alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get > > distinct colors for each type by default. But if the same pdb file is > > open with PyMOL all helices are treated the same way. Can't PyMOL > > distinguish helix types? > > Thanks in advance, > > Ramiro Téllez Sanz > > Dept. Physical Chemistry > > University of Almeria > > Spain > > ------------------------------------------------------------------------------ > > Xperia(TM) PLAY > > It's a major breakthrough. An authentic gaming > > smartphone on the nation's most reliable network. > > And it wants your games. > > http://p.sf.net/sfu/verizon-sfdev > > _______________________________________________ > > 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 > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > artforscience > H. Adam Steinberg > Artist, Scientist, Developmental Editor > www.artforscience.com > 7904 Bowman Rd > Lodi, WI 53555 > 608/729-5944 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
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From: Jason V. <jas...@sc...> - 2011-05-02 21:17:24
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Hi Maia,
Just use 'preset.function_name("(sele)")'. For example:
# fetch a protein, "1foo"
fetch 1foo, async=0
# call b-factor-putty on "1foo"
preset.b_factor_putty("(1foo)")
Cheers,
-- Jason
On Mon, May 2, 2011 at 4:46 PM, Maia Cherney <mch...@sh...> wrote:
> Dear Pymolers,
>
> I would like to be able to write a script with the a command that is
> available in actions (preset, pretty).
>
> How to do that?
>
> Maia
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120
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