From: s d. <sda...@gm...> - 2010-08-15 04:07:22
|
Dear All The default setting for color of inside of helices is grey. I am trying to color helices the same, both inside and outside. I tried using cartoon_highlight_color, blue but that does not change the grey to blue. Any help would be greatly appreciated. Thanks sdat5885 |
From: Vitaly V. <vv...@ua...> - 2010-08-15 04:40:45
|
Hello, I think this is the correct syntax: set cartoon_highlight_color, blue Vitaly ----- Original Message ----- From: s dat <sda...@gm...> Date: Saturday, August 14, 2010 11:08 pm Subject: [PyMOL] Newbie question : what command to use for changing color of inside of helix To: pym...@li... > Dear All > > The default setting for color of inside of helices is grey. I am > trying to > color helices the same, both inside and outside. I tried using > cartoon_highlight_color, blue but that does not change the grey to > blue. Any > help would be greatly appreciated. > > Thanks > sdat5885 > |
From: s d. <sda...@gm...> - 2010-08-15 05:26:20
|
Dear All set cartoon_highlight_color, blue does not change anything in my figure. If I the type set cartoon_highlight_color, -1 I get the following message: Setting: cartoon_highlight_color set to default. The default right now is grey. I tried to go into settings, change the default to for ex blue, and then tried to recolor but nothing happened ! Thanks sdat5885 On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> wrote: > Hello, > > I think this is the correct syntax: > set cartoon_highlight_color, blue > > > Vitaly > > ----- Original Message ----- > From: s dat <sda...@gm...> > Date: Saturday, August 14, 2010 11:08 pm > Subject: [PyMOL] Newbie question : what command to use for changing color > of inside of helix > To: pym...@li... > > > Dear All > > > > The default setting for color of inside of helices is grey. I am > > trying to > > color helices the same, both inside and outside. I tried using > > cartoon_highlight_color, blue but that does not change the grey to > > blue. Any > > help would be greatly appreciated. > > > > Thanks > > sdat5885 > > > |
From: Jason V. <jas...@sc...> - 2010-08-16 01:45:09
|
Vitaly is right, "set cartoon_highlight_color, blue" will set the inside helical color to blue. If you're having problems, please let us know which version of PyMOL you're using and on which OS (including version). Cheers, -- Jason On Sun, Aug 15, 2010 at 1:26 AM, s dat <sda...@gm...> wrote: > Dear All > > set cartoon_highlight_color, blue does not change anything in my figure. If > I the type set cartoon_highlight_color, -1 I get the following message: > Setting: cartoon_highlight_color set to default. > > The default right now is grey. I tried to go into settings, change the > default to for ex blue, and then tried to recolor but nothing happened ! > > Thanks > sdat5885 > > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> wrote: >> >> Hello, >> >> I think this is the correct syntax: >> set cartoon_highlight_color, blue >> >> >> Vitaly >> >> ----- Original Message ----- >> From: s dat <sda...@gm...> >> Date: Saturday, August 14, 2010 11:08 pm >> Subject: [PyMOL] Newbie question : what command to use for changing color >> of inside of helix >> To: pym...@li... >> >> > Dear All >> > >> > The default setting for color of inside of helices is grey. I am >> > trying to >> > color helices the same, both inside and outside. I tried using >> > cartoon_highlight_color, blue but that does not change the grey to >> > blue. Any >> > help would be greatly appreciated. >> > >> > Thanks >> > sdat5885 >> > > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: s d. <sda...@gm...> - 2010-08-16 04:50:00
|
Hi Jason Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP Professional 2002 SP3. Thanks for the help, Sdat5885 On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees < jas...@sc...> wrote: > Vitaly is right, > > "set cartoon_highlight_color, blue" > > will set the inside helical color to blue. If you're having problems, > please let us know which version of PyMOL you're using and on which OS > (including version). > > Cheers, > > -- Jason > > On Sun, Aug 15, 2010 at 1:26 AM, s dat <sda...@gm...> wrote: > > Dear All > > > > set cartoon_highlight_color, blue does not change anything in my figure. > If > > I the type set cartoon_highlight_color, -1 I get the following message: > > Setting: cartoon_highlight_color set to default. > > > > The default right now is grey. I tried to go into settings, change the > > default to for ex blue, and then tried to recolor but nothing happened ! > > > > Thanks > > sdat5885 > > > > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> > wrote: > >> > >> Hello, > >> > >> I think this is the correct syntax: > >> set cartoon_highlight_color, blue > >> > >> > >> Vitaly > >> > >> ----- Original Message ----- > >> From: s dat <sda...@gm...> > >> Date: Saturday, August 14, 2010 11:08 pm > >> Subject: [PyMOL] Newbie question : what command to use for changing > color > >> of inside of helix > >> To: pym...@li... > >> > >> > Dear All > >> > > >> > The default setting for color of inside of helices is grey. I am > >> > trying to > >> > color helices the same, both inside and outside. I tried using > >> > cartoon_highlight_color, blue but that does not change the grey to > >> > blue. Any > >> > help would be greatly appreciated. > >> > > >> > Thanks > >> > sdat5885 > >> > > > > > > > > ------------------------------------------------------------------------------ > > This SF.net email is sponsored by > > > > Make an app they can't live without > > Enter the BlackBerry Developer Challenge > > http://p.sf.net/sfu/RIM-dev2dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) Jas...@sc... > (o) +1 (603) 374-7120 > |
From: Tsjerk W. <ts...@gm...> - 2010-08-16 07:54:15
|
Hi Sdat5885, Have you started a fresh session, or did you a. load a session file or b. did some other things you didn't mention before? It may be that you have specifically set the highlight color for your protein. The default is not grey, but whatever color the C alpha atom has. You might want to try: set cartoon_highlight_color, blue, object_to_highlight Cheers, Tsjerk On Mon, Aug 16, 2010 at 6:49 AM, s dat <sda...@gm...> wrote: > Hi Jason > > Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP > Professional 2002 SP3. > > Thanks for the help, > Sdat5885 > > On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees > <jas...@sc...> wrote: >> >> Vitaly is right, >> >> "set cartoon_highlight_color, blue" >> >> will set the inside helical color to blue. If you're having problems, >> please let us know which version of PyMOL you're using and on which OS >> (including version). >> >> Cheers, >> >> -- Jason >> >> On Sun, Aug 15, 2010 at 1:26 AM, s dat <sda...@gm...> wrote: >> > Dear All >> > >> > set cartoon_highlight_color, blue does not change anything in my figure. >> > If >> > I the type set cartoon_highlight_color, -1 I get the following message: >> > Setting: cartoon_highlight_color set to default. >> > >> > The default right now is grey. I tried to go into settings, change the >> > default to for ex blue, and then tried to recolor but nothing happened ! >> > >> > Thanks >> > sdat5885 >> > >> > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> >> > wrote: >> >> >> >> Hello, >> >> >> >> I think this is the correct syntax: >> >> set cartoon_highlight_color, blue >> >> >> >> >> >> Vitaly >> >> >> >> ----- Original Message ----- >> >> From: s dat <sda...@gm...> >> >> Date: Saturday, August 14, 2010 11:08 pm >> >> Subject: [PyMOL] Newbie question : what command to use for changing >> >> color >> >> of inside of helix >> >> To: pym...@li... >> >> >> >> > Dear All >> >> > >> >> > The default setting for color of inside of helices is grey. I am >> >> > trying to >> >> > color helices the same, both inside and outside. I tried using >> >> > cartoon_highlight_color, blue but that does not change the grey to >> >> > blue. Any >> >> > help would be greatly appreciated. >> >> > >> >> > Thanks >> >> > sdat5885 >> >> > >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > This SF.net email is sponsored by >> > >> > Make an app they can't live without >> > Enter the BlackBerry Developer Challenge >> > http://p.sf.net/sfu/RIM-dev2dev >> > _______________________________________________ >> > 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 > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands |
From: s d. <sda...@gm...> - 2010-08-16 19:31:18
|
Hi Tsjerk Now it DOES change the color of the inside of helixes. Thank you so much. I think this is what happened. I was using the preset publication command to generate cartoons and then changing things. Once preset publication is invoked the command set cartoon_highlight_color, blue does not change anything. When I tried to use what you suggested on the same file (set cartoon_highlight_color, blue, helix A) it changed the color for the whole molecule, not just helix A. So I started with a fresh pdb file and now it seems that by default pymol colors the inside and outside of the helix the same. And when I make selections and change colors for that selection, the changes including the colors of the inside of the helix are confined to that selection. Thank you again, it was driving me nuts. sdat5885 On Mon, Aug 16, 2010 at 12:54 AM, Tsjerk Wassenaar <ts...@gm...>wrote: > Hi Sdat5885, > > Have you started a fresh session, or did you a. load a session file or > b. did some other things you didn't mention before? It may be that you > have specifically set the highlight color for your protein. The > default is not grey, but whatever color the C alpha atom has. You > might want to try: > > set cartoon_highlight_color, blue, object_to_highlight > > Cheers, > > Tsjerk > > On Mon, Aug 16, 2010 at 6:49 AM, s dat <sda...@gm...> wrote: > > Hi Jason > > > > Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP > > Professional 2002 SP3. > > > > Thanks for the help, > > Sdat5885 > > > > On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees > > <jas...@sc...> wrote: > >> > >> Vitaly is right, > >> > >> "set cartoon_highlight_color, blue" > >> > >> will set the inside helical color to blue. If you're having problems, > >> please let us know which version of PyMOL you're using and on which OS > >> (including version). > >> > >> Cheers, > >> > >> -- Jason > >> > >> On Sun, Aug 15, 2010 at 1:26 AM, s dat <sda...@gm...> wrote: > >> > Dear All > >> > > >> > set cartoon_highlight_color, blue does not change anything in my > figure. > >> > If > >> > I the type set cartoon_highlight_color, -1 I get the following > message: > >> > Setting: cartoon_highlight_color set to default. > >> > > >> > The default right now is grey. I tried to go into settings, change the > >> > default to for ex blue, and then tried to recolor but nothing happened > ! > >> > > >> > Thanks > >> > sdat5885 > >> > > >> > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> > >> > wrote: > >> >> > >> >> Hello, > >> >> > >> >> I think this is the correct syntax: > >> >> set cartoon_highlight_color, blue > >> >> > >> >> > >> >> Vitaly > >> >> > >> >> ----- Original Message ----- > >> >> From: s dat <sda...@gm...> > >> >> Date: Saturday, August 14, 2010 11:08 pm > >> >> Subject: [PyMOL] Newbie question : what command to use for changing > >> >> color > >> >> of inside of helix > >> >> To: pym...@li... > >> >> > >> >> > Dear All > >> >> > > >> >> > The default setting for color of inside of helices is grey. I am > >> >> > trying to > >> >> > color helices the same, both inside and outside. I tried using > >> >> > cartoon_highlight_color, blue but that does not change the grey to > >> >> > blue. Any > >> >> > help would be greatly appreciated. > >> >> > > >> >> > Thanks > >> >> > sdat5885 > >> >> > > >> > > >> > > >> > > >> > > ------------------------------------------------------------------------------ > >> > This SF.net email is sponsored by > >> > > >> > Make an app they can't live without > >> > Enter the BlackBerry Developer Challenge > >> > http://p.sf.net/sfu/RIM-dev2dev > >> > _______________________________________________ > >> > 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 > > > > > > > ------------------------------------------------------------------------------ > > This SF.net email is sponsored by > > > > Make an app they can't live without > > Enter the BlackBerry Developer Challenge > > http://p.sf.net/sfu/RIM-dev2dev > > _______________________________________________ > > PyMOL-users mailing list (PyM...@li...) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pym...@li... > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology / > University of Groningen > The Netherlands > |
From: Jason V. <jas...@sc...> - 2010-08-16 19:39:23
|
> I think this is what happened. I was using the preset publication command to Oh, you didn't tell us that! Think of the presets from A->Action->Preset-> menus, as end-points to visualization: don't try to change settings after you apply one of these. These are somewhat complex scripts under the hood and change many settings, some of which are nearly impossible to recover. Actually, I fell into this trap a few years ago. Warren would just tell me the same thing: don't try changing the settings once you've used these commands. Cheers, -- Jason On Mon, Aug 16, 2010 at 3:31 PM, s dat <sda...@gm...> wrote: > Hi Tsjerk > > Now it DOES change the color of the inside of helixes. Thank you so much. > > I think this is what happened. I was using the preset publication command to > generate cartoons and then changing things. Once preset publication is > invoked the command set cartoon_highlight_color, blue does not change > anything. When I tried to use what you suggested on the same file (set > cartoon_highlight_color, blue, helix A) it changed the color for the whole > molecule, not just helix A. > > So I started with a fresh pdb file and now it seems that by default pymol > colors the inside and outside of the helix the same. And when I make > selections and change colors for that selection, the changes including the > colors of the inside of the helix are confined to that selection. > > Thank you again, it was driving me nuts. > > sdat5885 > > > > On Mon, Aug 16, 2010 at 12:54 AM, Tsjerk Wassenaar <ts...@gm...> > wrote: >> >> Hi Sdat5885, >> >> Have you started a fresh session, or did you a. load a session file or >> b. did some other things you didn't mention before? It may be that you >> have specifically set the highlight color for your protein. The >> default is not grey, but whatever color the C alpha atom has. You >> might want to try: >> >> set cartoon_highlight_color, blue, object_to_highlight >> >> Cheers, >> >> Tsjerk >> >> On Mon, Aug 16, 2010 at 6:49 AM, s dat <sda...@gm...> wrote: >> > Hi Jason >> > >> > Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP >> > Professional 2002 SP3. >> > >> > Thanks for the help, >> > Sdat5885 >> > >> > On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees >> > <jas...@sc...> wrote: >> >> >> >> Vitaly is right, >> >> >> >> "set cartoon_highlight_color, blue" >> >> >> >> will set the inside helical color to blue. If you're having problems, >> >> please let us know which version of PyMOL you're using and on which OS >> >> (including version). >> >> >> >> Cheers, >> >> >> >> -- Jason >> >> >> >> On Sun, Aug 15, 2010 at 1:26 AM, s dat <sda...@gm...> wrote: >> >> > Dear All >> >> > >> >> > set cartoon_highlight_color, blue does not change anything in my >> >> > figure. >> >> > If >> >> > I the type set cartoon_highlight_color, -1 I get the following >> >> > message: >> >> > Setting: cartoon_highlight_color set to default. >> >> > >> >> > The default right now is grey. I tried to go into settings, change >> >> > the >> >> > default to for ex blue, and then tried to recolor but nothing >> >> > happened ! >> >> > >> >> > Thanks >> >> > sdat5885 >> >> > >> >> > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vv...@ua...> >> >> > wrote: >> >> >> >> >> >> Hello, >> >> >> >> >> >> I think this is the correct syntax: >> >> >> set cartoon_highlight_color, blue >> >> >> >> >> >> >> >> >> Vitaly >> >> >> >> >> >> ----- Original Message ----- >> >> >> From: s dat <sda...@gm...> >> >> >> Date: Saturday, August 14, 2010 11:08 pm >> >> >> Subject: [PyMOL] Newbie question : what command to use for changing >> >> >> color >> >> >> of inside of helix >> >> >> To: pym...@li... >> >> >> >> >> >> > Dear All >> >> >> > >> >> >> > The default setting for color of inside of helices is grey. I am >> >> >> > trying to >> >> >> > color helices the same, both inside and outside. I tried using >> >> >> > cartoon_highlight_color, blue but that does not change the grey to >> >> >> > blue. Any >> >> >> > help would be greatly appreciated. >> >> >> > >> >> >> > Thanks >> >> >> > sdat5885 >> >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > ------------------------------------------------------------------------------ >> >> > This SF.net email is sponsored by >> >> > >> >> > Make an app they can't live without >> >> > Enter the BlackBerry Developer Challenge >> >> > http://p.sf.net/sfu/RIM-dev2dev >> >> > _______________________________________________ >> >> > 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 >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > This SF.net email is sponsored by >> > >> > Make an app they can't live without >> > Enter the BlackBerry Developer Challenge >> > http://p.sf.net/sfu/RIM-dev2dev >> > _______________________________________________ >> > PyMOL-users mailing list (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pym...@li... >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> Groningen Institute for Biomolecular Research and Biotechnology / >> University of Groningen >> The Netherlands > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |