I tried that.
that is actually how I found this is a way to color them according the CA color
assigned in the spectrum.
Charles
________________________________
From: Olson, Linda <lol...@mcw.edu>
Sent: Thursday, May 21, 2020 12:24 PM
To: Chen, Qiang <q...@pitt.edu>
Subject: Re: Consistent coloring between sticks of sidechains and cartoon
backbones in spectrum coloring
Have you tried going to the first option under the color by menu which colors c
alpha by whatever they are asigned?
Linda Olson, PhD
Assistant Professor/
x-Ray Facility Manager
Dept. Biochemistry
Medical College of Wisconsin
8701 Watertown Plank Rd
Milwaukee, WI 53226
phone 414-955-8545
fax 414-456-6510
________________________________
From: Chen, Qiang <q...@pitt.edu>
Sent: Thursday, May 21, 2020 10:20:11 AM
To: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>;
pymol-users@lists.sourceforge.net <pymol-users@lists.sourceforge.net>
Subject: Re: [PyMOL] Consistent coloring between sticks of sidechains and
cartoon backbones in spectrum coloring
ATTENTION: This email originated from a sender outside of MCW. Use caution when
clicking on links or opening attachments.
________________________________
Thanks, Prof. Mooers.
I tried your script. It did not report any error. but the selected residues are
colored as the default, green for carbon.
Then I figured out I made things complicated.
I created a new object (cnsp) for the cartoon representation colored with
spectrum.
Then I selected residues with chain A and resi 10+20+30, and showed them as
sticks. I guess, the color info of CAs from the spectrum is missing at this
step.
If I selected the residues with cnsp and chain A and resi 10+20+30, then showed
them with sticks, the color of sidechain is matching with CA color in the
spectrum.
All I need is just util.cnc.
The working script is like the following
select cnsp, chain A
spectrum count, magenta_cyan, cnsp, byres=1
select sre, cnsp and resi 10+20+30
show sticks, sre,
util.cnc sre
Charles
________________________________
From: Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>
Sent: Thursday, May 21, 2020 9:19 AM
To: Chen, Qiang <q...@pitt.edu>; pymol-users@lists.sourceforge.net
<pymol-users@lists.sourceforge.net>
Subject: RE: Consistent coloring between sticks of sidechains and cartoon
backbones in spectrum coloring
Hi Charles,
This pml script does want you want,
# Color the carvons atoms of the sidechain the same as the color of the CA atom
col=[]
# >>>> edit resi here
iterate resi 10+20+30 and name ca,
col.append((chain,resi,name,cmd.get_color_tuple(color)))
# Define the colors ca10, ca20, and ca40
[cmd.set_color('ca'+co[1],list(co[3]) ) for co in col]
# >>>>>>Edit color names here
colorList =['ca10','ca20','ca30']
# Check this list
[print(cmd.get_color_tuple(co)) for co in colorList]
#make a list of residues
resList = [co[1] for co in col]
# Check the list
print(resList)
# Now zip the list of colors and the list of residues
pairs = list(zip(colorList,resList))
# Check the list of lists
print(pairs)
# Check the atom selection syntax
[print('resi ' + str(pairs[i][1]) + ' and (sidechain and name c*)') for i in
range(0,len(pairs))]
# Apply the pairs after defining the indices
[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1]) + ' and (sidechain and name
c*)') for i in range(0,len(pairs))]
The print statements are sanity checks.
You can delete them and the comments if you want a more concise script.
You can also copy and paste this compound command onto the command line to get
the get effect.
You the up arrow key to get back the command and edit the list of residues and
the colorList.
col=[];iterate resi 10+20+30 and name ca,
col.append((chain,resi,name,cmd.get_color_tuple(color)));colorList
=['ca10','ca20','ca30'];resList = [co[1] for co in col];pairs =
list(zip(colorList,resList));[cmd.color(pairs[i][0], 'resi ' + str(pairs[i][1])
+ ' and (sidechain and name c*)') for i in range(0,len(pairs))]
When you enter help color, you will see that the first argument of color is the
color, which is a string.
That string is a name or number. The number is an integer that is internally
mapped to a color name.
You can see these by entering the following: print(cmd.get_color_indices()).
Your col object is a list of tuples.
This is not of the data type that the color command expects.
The third line of your code returns an error because col is a list of tuples
and not a string.
That number is not the same as your color tuple.
You want to apply your color tuple.
I am not sure how to do apply the color tuple because PyMOL will take the RGB
values as list of integers, not as a tuple.
The returned tuple is for use in an external program.
The above script converts the tuple into a list of integers that PyMOL can work
with.
Best regards,
Blaine
Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419
________________________________________
From: Chen, Qiang [q...@pitt.edu]
Sent: Wednesday, May 20, 2020 7:50 PM
To: pymol-users@lists.sourceforge.net
Subject: [EXTERNAL] [PyMOL] Consistent coloring between sticks of sidechains
and cartoon backbones in spectrum coloring
Hi, Pymol-users
I have my protein shown as cartoon and colored with spectrum. Now I would like
to show several residues at different places with sticks representation. when I
tried, I can not get the color consistent between the backbone CA and the
carbons on the sidechain.
I searched the archives, and tried something like this.
col=[]
iterate resi 10+20+30 and name ca,
col.append((chain,resi,name,cmd.get_color_tuple(color)))
cmd.color(col,"all")
util.cnc("all")
The first two lines will get me a color_tuple of the selected residues (CA)
The third line will color all atoms as the same color of CA.
The fourth line will color all none carbon atoms with the default colors.
However, this does not work as I thought.
Would anyone point out what mistakes I made here? Or any other solution to get
the consistence between CA and the sidechain?
Your help is high appreciated!
Thanks!
Charles
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