Thread: [Apbs-users] Change slice contour levels in APBS/pymol?
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From: David B. <dav...@al...> - 2011-03-15 20:42:15
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Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? Thanks! Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 David.Borhani@DEShawResearch.com 212-478-0698 http://www.deshawresearch.com |
From: Borhani, D. <David.Borhani@DEShawResearch.com> - 2011-03-15 19:54:59
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Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? Thanks! Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 David.Borhani@DEShawResearch.com<mailto:David.Borhani@DEShawResearch.com> 212-478-0698 http://www.deshawresearch.com |
From: Harmon, T. S <Tyl...@pn...> - 2011-03-16 18:17:35
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If you are using the plug in menu then after you have run apbs, it shows the visualization menu where the bottom middle and bottom right boxes are the isosurfaces options. There is an adjustable box for each that changes the potential of the contour. After it is already displaying the contour you can click on the color menu on the main display and choose any color that you want. Let me know if that doesn't help, Tyler From: Borhani, David [mailto:David.Borhani@DEShawResearch.com] Sent: Tuesday, March 15, 2011 12:42 PM To: 'apb...@li...' Subject: [Apbs-users] Change slice contour levels in APBS/pymol? Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? Thanks! Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 David.Borhani@DEShawResearch.com<mailto:David.Borhani@DEShawResearch.com> 212-478-0698 http://www.deshawresearch.com |
From: Borhani, D. <David.Borhani@DEShawResearch.com> - 2011-03-17 03:00:24
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Thanks, Tyler. One thing I don't understand about what you wrote: when you pick a color on an already-displayed contour, which color (of the usual 3 colors in the ramp) gets set? And how does this affect the colors in a slice instead? I updated the Pymol Wiki with what I figured out (with help from Keith Callenberg). See: http://www.pymolwiki.org/index.php/Slice. Detailed instructions on one way to do what I wanted (there may be a better way!) It's Example #2 (with an illustrative image). Thanks for your help, Dave From: Harmon, Tyler S [mailto:Tyl...@pn...] Sent: Wednesday, 16 March 2011 14:17 To: Borhani, David; 'apb...@li...' Subject: RE: Change slice contour levels in APBS/pymol? If you are using the plug in menu then after you have run apbs, it shows the visualization menu where the bottom middle and bottom right boxes are the isosurfaces options. There is an adjustable box for each that changes the potential of the contour. After it is already displaying the contour you can click on the color menu on the main display and choose any color that you want. Let me know if that doesn't help, Tyler From: Borhani, David [mailto:David.Borhani@DEShawResearch.com] Sent: Tuesday, March 15, 2011 12:42 PM To: 'apb...@li...' Subject: [Apbs-users] Change slice contour levels in APBS/pymol? Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? Thanks! Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 David.Borhani@DEShawResearch.com<mailto:David.Borhani@DEShawResearch.com> 212-478-0698 http://www.deshawresearch.com |
From: Harmon, T. S <Tyl...@pn...> - 2011-03-17 17:11:15
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Dave, I misunderstood what you were asking for. To change the color you have to redefine the color ramp as you described in the pymol wiki. From: Borhani, David [mailto:David.Borhani@DEShawResearch.com] Sent: Wednesday, March 16, 2011 8:00 PM To: Harmon, Tyler S; 'apb...@li...' Subject: RE: Change slice contour levels in APBS/pymol? Thanks, Tyler. One thing I don't understand about what you wrote: when you pick a color on an already-displayed contour, which color (of the usual 3 colors in the ramp) gets set? And how does this affect the colors in a slice instead? I updated the Pymol Wiki with what I figured out (with help from Keith Callenberg). See: http://www.pymolwiki.org/index.php/Slice. Detailed instructions on one way to do what I wanted (there may be a better way!) It's Example #2 (with an illustrative image). Thanks for your help, Dave From: Harmon, Tyler S [mailto:Tyl...@pn...] Sent: Wednesday, 16 March 2011 14:17 To: Borhani, David; 'apb...@li...' Subject: RE: Change slice contour levels in APBS/pymol? If you are using the plug in menu then after you have run apbs, it shows the visualization menu where the bottom middle and bottom right boxes are the isosurfaces options. There is an adjustable box for each that changes the potential of the contour. After it is already displaying the contour you can click on the color menu on the main display and choose any color that you want. Let me know if that doesn't help, Tyler From: Borhani, David [mailto:David.Borhani@DEShawResearch.com] Sent: Tuesday, March 15, 2011 12:42 PM To: 'apb...@li...' Subject: [Apbs-users] Change slice contour levels in APBS/pymol? Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? Thanks! Dave David Borhani, Ph.D. D. E. Shaw Research 120 West Forty-Fifth Street, 39th Floor New York, NY 10036 David.Borhani@DEShawResearch.com<mailto:David.Borhani@DEShawResearch.com> 212-478-0698 http://www.deshawresearch.com |
From: Keith C. <km...@pi...> - 2011-03-15 21:11:07
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Hi Dave, I'm not sure about the contours, but for the colors: ramp_new e_lvl, apbs_map, [-10,0,10], [ [0,1,0], [1,1,1], [1,0,0] ] where the first array is for your scale and the second array is for your 3 colors in RGB (on a scale of 0 to 1). Keith On Tue, Mar 15, 2011 at 4:04 PM, David Borhani <dav...@al...> wrote: > Is there a way to change the default slice contours of ±1 kT/e shown by ABPS plugin in pymol, as you can for the isosrufaces and the molecular surface? Also, how does one change the colors? > > Thanks! > Dave > > David Borhani, Ph.D. > D. E. Shaw Research > 120 West Forty-Fifth Street, 39th Floor > New York, NY 10036 > David.Borhani@DEShawResearch.com > 212-478-0698 > http://www.deshawresearch.com > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Keith M. Callenberg Carnegie Mellon-University of Pittsburgh Program in Computational Biology kmc112@{pitt,cmu}.edu http://www.pitt.edu/~kmc112/ -- Keith M. Callenberg Carnegie Mellon-University of Pittsburgh Program in Computational Biology kmc112@{pitt,cmu}.edu http://www.pitt.edu/~kmc112/ |