Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?
Hello, Marko, Think you for your reply. I can use the bar object "Action" > "Levels" to set the levels/scales to -100~100, but could you tell me what are the units for the values? Best regards -- From:Marko Hyvonen Sent At:2019 Sep. 12 (Thu.) 15:58 To:pymol-users Subject:Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics? Hi Yeping, Click on the bar object "Action" > "Levels" for a few preset levels/scales. hth, Marko On 12/09/2019 08:03, sunyeping via PyMOL-users wrote: Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping ___ 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 -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk ___ 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] PyMol: incomplete replacement of b- and q-factors
Hello all, I am trying to color several proteins by different factors, e.g., distance from a given point (here the origin). To do this, I replace the q-factor (or b-factor) with my variable of choice. However, most of my files have one or a few residues that are for some reason not affected by the alter_state (e.g., pdb = 1ihm). I can't see any distinction in these residues compared to the others. example code: fetch 1ihm alldist = [] iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5) di = iter(alldist) alter all, b = next(di) spectrum b Thank you, Joe ___ 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] How to manually define the lower and upper limit of vacuum electrostatics?
Hi Yeping, Click on the bar object "Action" > "Levels" for a few preset levels/scales. hth, Marko On 12/09/2019 08:03, sunyeping via PyMOL-users wrote: Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping ___ 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 -- Marko Hyvonen Department of Biochemistry, University of Cambridge mh...@cam.ac.uk +44 (0)1223 766 044 @HyvonenGroup http://hyvonen.bioc.cam.ac.uk ___ 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] How to manually define the lower and upper limit of vacuum electrostatics?
Dear all, I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively. I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared? Best regards. Yeping___ 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
