Re: [PyMOL] ribbon-like with one color

2006-10-06 Thread Mario Sanches
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=palette_name, selection=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




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--
Mario Sanches
Laboratório Nacional de Luz Síncrotron
Cristalografia e Espectroscopia de Biomoléculas
Tel: +55 19 3512 1109




Re: [PyMOL] ribbon-like with one color

2006-10-05 Thread Mario Sanches
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




[PyMOL] ribbon-like with one color

2006-10-04 Thread Mario Sanches
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