[PyMOL] Display of electrostatic potential surfaces
Dear PyMOL users,
I would like to generate a figure of my protein where the surface electrostatic
potential is displayed. PyMOL now comes with a demo function for display of
such a surface. However, when I apply the commands used in this demo, i.e.
cmd.set("coulomb_dielectric",80.0)
cmd.map_new("e_pot","coulomb",1.0,"pept",5)
cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
cmd.set("surface_color","e_lvl","pept")
cmd.refresh()
to the model from my pdb file, I get a uniformly blue surface. I believe this
must be due to the lack of assignment of partial/formal charges to the atoms in
the pdb file. So, my questions are:
1. Is it possible to automatically assign the correct charges to atoms within
PyMOL
2. If not, is there a program that will do this and if so can the output from
this program be understood by PyMOL in some way.
Thanks for your help
Roger
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge
RE: [PyMOL] Display of electrostatic potential surfaces
Roger,
The problem with computing electrostatic maps in PyMOL
currently is that the Coulomb equation assumes a uniform dielectric and
thus doesn't give you correct potentials for macromolecules. It is much
better to use an external tool such as Grasp, MEAD, APBS, or Delphi,
which can apply a different dielectric constant to the inside of the
protein than to the surrounding solvent.
Yes, PyMOL can compute a Coulombic map using the approach
you've outlined if partial charges have been assigned - but there isn't
a good way to do that in PyMOL just yet.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Roger Dodd
Sent: Thursday, December 18, 2003 3:53 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Display of electrostatic potential surfaces
Dear PyMOL users,
I would like to generate a figure of my protein where the surface
electrostatic potential is displayed. PyMOL now comes with a demo
function for display of such a surface. However, when I apply the
commands used in this demo, i.e.
cmd.set("coulomb_dielectric",80.0)
cmd.map_new("e_pot","coulomb",1.0,"pept",5)
cmd.ramp_new("e_lvl","e_pot",[-3.6,-1.6,0.4])
cmd.set("surface_color","e_lvl","pept")
cmd.refresh()
to the model from my pdb file, I get a uniformly blue surface. I believe
this must be due to the lack of assignment of partial/formal charges to
the atoms in the pdb file. So, my questions are:
1. Is it possible to automatically assign the correct charges to atoms
within PyMOL
2. If not, is there a program that will do this and if so can the output
from this program be understood by PyMOL in some way.
Thanks for your help
Roger
--
Roger Dodd
CIMR
Addenbrooke's Hospital
Cambridge
[PyMOL] RE: 3-button mice
Chris, I hereby nominate the Targus PAUM01U as the official 3-button mouse for PyMOL users on the go. http://www.targus.com/us/product_details.asp?sku=PAUM01U They might be too small for some, but they work great for me, at home and on the road! (plus, they color-coordinate with Ti PowerBooks) Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- Sent: Thursday, December 18, 2003 5:45 AM To: war...@delanoscientific.com Subject: pymol Hi, I plan to update the website (http://www.macinchem.fsnet.co.uk) over the Christmas Break and one question I'm often asked is which 3-button mouse should I use for PYMOL under MacOSX? Any suggestions? Thanks Chris
[PyMOL] unsetting cartoon_colors
Hi all, I have a collection of molecules and want to color a particular helix (in cartoon mode) a specific color different from other helices. Unfortunately, I had previously set cartoon_color from "default" to another color, so now specifying a color for that helix (or even "color red, ss h") has no impact. (it does change the color of the Calpha, but not the cartoon itself). So, the question is, how do I unset the cartoon_color variable (without wiping out my scene)? The variable setting comes with the .pse file, "set cartoon_color, default" gives an error about not knowing what color default is. Thanks, Dave Horita - 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://www.wfubmc.edu/biochem/faculty/Horita/
RE: [PyMOL] unsetting cartoon_colors
David, For settings such as cartoon_color, surface_color, mesh_color, the default value is -1. set cartoon_color, -1 or set cartoon_color, -1, object-name will restore the color. Thanks for pointing out that: set cartoon_color, default doesn't work! Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of David A. Horita Sent: Thursday, December 18, 2003 10:50 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] unsetting cartoon_colors Hi all, I have a collection of molecules and want to color a particular helix (in cartoon mode) a specific color different from other helices. Unfortunately, I had previously set cartoon_color from "default" to another color, so now specifying a color for that helix (or even "color red, ss h") has no impact. (it does change the color of the Calpha, but not the cartoon itself). So, the question is, how do I unset the cartoon_color variable (without wiping out my scene)? The variable setting comes with the .pse file, "set cartoon_color, default" gives an error about not knowing what color default is. Thanks, Dave Horita - 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://www.wfubmc.edu/biochem/faculty/Horita/
