Re: [PyMOL] ribbon-like with one color
Thank you for that tip Mark. Using those palettes I managed to compose the cartoon that I wanted. Thank you all that sent me scripts and tips. All the best, Mario Sanches Mark A Saper wrote: There are actually other spectrums built into the PyMOL. To use one of them, type spectrum palette=, selection= The list of built-in palettes are in cmd.py of the code. All seem to be multi color; so there are none that are just different shades of one color. _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html Biophysics Interdepartmental Graduate Program: http://www.umich.edu/ ~biophys - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Mario Sanches Laboratório Nacional de Luz Síncrotron Cristalografia e Espectroscopia de Biomoléculas Tel: +55 19 3512 1109
Re: [PyMOL] ribbon-like with one color
There are actually other spectrums built into the PyMOL. To use one of them, type spectrum palette=, selection= The list of built-in palettes are in cmd.py of the code. All seem to be multi color; so there are none that are just different shades of one color. _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan Chemistry Building Room 3040 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu(734) 764-3353fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html Biophysics Interdepartmental Graduate Program: http://www.umich.edu/ ~biophys
Re: [PyMOL] ribbon-like with one color
Thank you for the script Andreas, it worked fine. Now, is there any way
to define wich objet is going to be colored? I want to use different
color hues for two different objects.
Thank you,
Mario Sanches
Andreas Henschel wrote:
Hi Mario,
you can define new colors wit the set_color command.
below are two python functions that can define ranges,
one using HSV color space, one RGB. The former is a derivite
of a script earlier posetd by Robert L. Campbell on the wiki.
Hope that helps.
Cheers, Andreas
def hueSpectrum(hue1=0.0, hue2=0.2, nbins=10, sat=1., value=1.):
## by default creates 10 shades of red
## Derived from color_b.py
## Author Robert L. Campbell, see pymol wiki
colorNames=[]
stepsize = (hue1 - hue2) / nbins
for j in range(nbins):
# for the selection
colorName = "hueSpectrum%02d"%(j)
colorNames.append(colorName)
hsv = (hue1 - stepsize * float(j), sat, value)
#convert to rgb and append to color list
rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
cmd.set_color(colorName, rgb)
return colorNames
def hueSpectrum2(r=1., g = .0, b = .0, shades=10, shadeSpec=0.4):
colorNames=[]
r0 = max(r - shadeSpec/2, 0.0)
g0 = max(g - shadeSpec/2, 0.0)
b0 = max(b - shadeSpec/2, 0.0)
stepsize = shadeSpec/(shades-1.)
for j in range(shades):
# for the selection
colorName = "hueSpectrum%02d"%(j)
colorNames.append(colorName)
r0 = min(r0+stepsize, 1.0)
g0 = min(g0+stepsize, 1.0)
b0 = min(b0+stepsize, 1.0)
cmd.set_color(colorName, (r0, g0, b0))
return colorNames
def colorSpec(residue1, residue2, shades=10):
## careful: assumes consecutive resi's ...
resiPerColor = abs(residue1-residue2)/shades
for j in range(residue2-residue1):
color = shades*j/(residue2-residue1) ## use only generated
shades. Careful: don't exceed!
cmd.color("hueSpectrum%02d" % color, "resi %s" %(residue1 + j) )
## usage: cmd.load("/group/bioinf/Data/PDBLinks/1god.pdb") ##
change path
cmd.as("cartoon")
cmd.color("white", "1god")
#hueSpectrum(0.5, 0.7) ## dark blue to cyan, looks cool, too!
hueSpectrum2() ## reddish
colorSpec(89, 109)
Mario Sanches wrote:
I am trying to color a structure with a ribbon like feature but not
going from blue to red, but instead, using differente blue hues (or
red hues, etc). Is that possible?
Thank,
--
Mario Sanches
Laboratório Nacional de Luz Síncrotron
Cristalografia e Espectroscopia de Biomoléculas
Tel: +55 19 3512 1109
Re: [PyMOL] ribbon-like with one color
Hi Mario,
you can define new colors wit the set_color command.
below are two python functions that can define ranges,
one using HSV color space, one RGB. The former is a derivite
of a script earlier posetd by Robert L. Campbell on the wiki.
Hope that helps.
Cheers, Andreas
def hueSpectrum(hue1=0.0, hue2=0.2, nbins=10, sat=1., value=1.):
## by default creates 10 shades of red
## Derived from color_b.py
## Author Robert L. Campbell, see pymol wiki
colorNames=[]
stepsize = (hue1 - hue2) / nbins
for j in range(nbins):
# for the selection
colorName = "hueSpectrum%02d"%(j)
colorNames.append(colorName)
hsv = (hue1 - stepsize * float(j), sat, value)
#convert to rgb and append to color list
rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
cmd.set_color(colorName, rgb)
return colorNames
def hueSpectrum2(r=1., g = .0, b = .0, shades=10, shadeSpec=0.4):
colorNames=[]
r0 = max(r - shadeSpec/2, 0.0)
g0 = max(g - shadeSpec/2, 0.0)
b0 = max(b - shadeSpec/2, 0.0)
stepsize = shadeSpec/(shades-1.)
for j in range(shades):
# for the selection
colorName = "hueSpectrum%02d"%(j)
colorNames.append(colorName)
r0 = min(r0+stepsize, 1.0)
g0 = min(g0+stepsize, 1.0)
b0 = min(b0+stepsize, 1.0)
cmd.set_color(colorName, (r0, g0, b0))
return colorNames
def colorSpec(residue1, residue2, shades=10):
## careful: assumes consecutive resi's ...
resiPerColor = abs(residue1-residue2)/shades
for j in range(residue2-residue1):
color = shades*j/(residue2-residue1) ## use only generated
shades. Careful: don't exceed!
cmd.color("hueSpectrum%02d" % color, "resi %s" %(residue1 + j) )
## usage:
cmd.load("/group/bioinf/Data/PDBLinks/1god.pdb") ## change path
cmd.as("cartoon")
cmd.color("white", "1god")
#hueSpectrum(0.5, 0.7) ## dark blue to cyan, looks cool, too!
hueSpectrum2() ## reddish
colorSpec(89, 109)
Mario Sanches wrote:
I am trying to color a structure with a ribbon like feature but not
going from blue to red, but instead, using differente blue hues (or red
hues, etc). Is that possible?
Thank,
--
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: a...@biotec.tu-dresden.de
