Re: [PyMOL] Color change of different domain

[Mohammad Goodarzi]

Hi John,

How can I add this to pymol on Mac? I don't see any plugin manager for mac
version, can you please put a comment ?

Thanks
Mohammad

On Thu, Aug 16, 2018 at 1:24 AM John Berrisford  wrote:

> Dear Mohammad
>
>
>
> Please see the PDB plugin which colours each sequence or structural domain
> differently.
>
> https://pymolwiki.org/index.php/PDB_plugin
>
>
>
> This is used to produce the images on the PDBe web pages.
>
> For example see a titin with multiple copies of a CATH domain.
>
> https://www.ebi.ac.uk/pdbe/entry/pdb/2rjm/biology
>
>
>
>
>
> Regards
>
>
>
> John
>
>
>
> *From:* Mohammad Goodarzi [mailto:mohammad.goda...@gmail.com]
> *Sent:* 08 August 2018 16:13
> *To:* pymol-users@lists.sourceforge.net
> *Subject:* [PyMOL] Color change of different domain
>
>
>
>
> I have a protein in PDB called "3E9D"
>
>
>
> I first get the seqeuence then I go here
> https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
>
> and I find the domains. Now I am trying to change the color accordingly
>
>
>
> Now I am trying to change the color of each domain with different color
> first I change the background to white
> bg_color white
> show cartoon
> hide lines
>
>
>
> Can you please tell me how to change the color of each domain to different
> colors ?
>
>
>
> Thanks
>
> Mohammad
>
>
>
>
>
>
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Re: [PyMOL] Color backbone amide nitrogen

[Marko Hyvonen]

  
  
The problem is that you are not visualising
  the backbone nitrogens. You
  only show the side chains as sticks and the
  backbone is shown as cartoons.These schematic
  representations of secondary structure are drawn using
Calpha atom positions and (typically)
  inherit the colour of the Calphas.  If
  you show the backbone as sticks, the nitrogens will be visible and
  they will have colour. Same goes for backbone oxygens
  which are similarly hidden in your image, but are coloured in the
  side chain at the bottom of the image. 

hth, Marko

On 23/07/2018 18:17, Santrupti Nerli
  wrote:


  
  Hi,
  
  
  I want to color backbone nitrogen atoms together
with side-chain nitrogen atoms. The side-chain nitrogens get the
color, however the backbone nitrogens don’t (see below; I have
selected backbone nitrogens). I tried some options such as
  
  
  select bb, name n
  color by element 
  
  
  
  
  
  But, the backbone nitrogens aren’t getting colored.
Is there a way to color them without showing them as spheres?
  
  
  Thanks a lot.
  
  
  
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Re: [PyMOL] Color bar for volume?

[Thomas Holder]

Hi Murpholino,

You could convert your volume colors to a ramp object with a Python script like 
this:

# conversion function
def volume2ramp(volname, rampname='', mapname='none'):
v = cmd.volume_color(volname)
colors = []
for i in range(0, len(v), 5):
colors.append('0x%02x%02x%02x' % (
int(v[i + 1] * 0xff),
int(v[i + 2] * 0xff),
int(v[i + 3] * 0xff)))
cmd.ramp_new(rampname or cmd.get_unused_name('ramp'),
mapname, v[0::5], colors)

# apply to your volume object
volume2ramp('myvolume')

Hope that helps.

Cheers,
  Thomas

> On Feb 6, 2018, at 3:36 PM, Murpholino Peligro  wrote:
> 
> Is there a way to add a color bar to a volume?
> I am looking for something like the bar in the last picture here 
> (https://pymolwiki.org/index.php/Ramp_New)
> This is my volume https://www.dropbox.com/s/x4ic7uvdlknk8us/volume.png?dl=0
> 
> 
> Thanks. 

--
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Color residue in cartoon mode

[harold steinberg]

I’m sorry, I thought she was trying to use two different cartoon modes and two 
different colors.


> On Aug 2, 2016, at 12:07 PM, Thomas Holder  
> wrote:
> 
> Hi Maria and Adam,
> 
> I think it's not that complicated. You need "cartoon_ring_mode" for the 
> residue selection. Example:
> 
> fetch 1rna, async=0
> as cartoon
> select firstres, chain A & resi 1
> set cartoon_ring_finder, 2
> set cartoon_ring_mode, 2, firstres
> color blue
> color red, firstres extend 1
> 
> Hope that helps.
> 
> Cheers,
>  Thomas
> 
> On 02 Aug 2016, at 12:42, harold steinberg  wrote:
> 
>> I believe that you can only apply the cartoon setting to an entire obj 
>> (object). And so you are correct in trying to duplicate the nucleotide so 
>> you can apply one setting to it, while allowing the other setting to display 
>> the rest of them. But that doesn’t work either since the program will only 
>> allow one display type at a time. There may be a complex way to override it 
>> but I do not know it.
>> 
>> The way I have gotten around this in the past is to set up the entire object 
>> the way you want it, then render it once with each setting.
>> 
>> Then open both of the resulting images in photoshop or similar program. Put 
>> them both into one file as layers.
>> 
>> Then delete most of one of the files (say the top one) so only the single 
>> nucleotide is left in the cartoon setting that you want in that layer. The 
>> rest of the image will appear from the bottom layer.
>> 
>> Then you can flatten the image and save it. It’s fast and works great.
>> 
>> 
>>> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
>>> wrote:
>>> 
>>> Dear pymol-users,
>>> 
>>> I’m still learning how to use pymol to do basic things.
>>> At present, I’m working with a nucleic acid molecule that is colored by 
>>> sequence domains (each domain is a different objet). All the domains are 
>>> displayed in the cartoon mode, with backbone as dumbbell and 
>>> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
>>> like to display only the first residue of one of the domains as 
>>> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  
>>> entirely (dumbbell + ribose stick + base ring) with a different color from 
>>> the rest of the domain sequence.  The problem is that it does not work ! 
>>> 
>>> I tried to copy that nucleotide into a new objet to manipulate it 
>>> independently but all the arguments I write in the command line do not 
>>> apply to it, nothing is changing on the screen. The only thing that works 
>>> is the menu on the right, use the objet line corresponding to this residue, 
>>> display it entirely as sticks and then change the color of the sticks. But 
>>> that’s not what I need!
>>> 
>>> Do you have any ideas how to display the desired nucleotide?
>>> 
>>> Many thanks in advance,
>>> 
>>> Maria
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] Color residue in cartoon mode

[Thomas Holder]

Hi Maria and Adam,

I think it's not that complicated. You need "cartoon_ring_mode" for the residue 
selection. Example:

fetch 1rna, async=0
as cartoon
select firstres, chain A & resi 1
set cartoon_ring_finder, 2
set cartoon_ring_mode, 2, firstres
color blue
color red, firstres extend 1

Hope that helps.

Cheers,
  Thomas

On 02 Aug 2016, at 12:42, harold steinberg  wrote:

> I believe that you can only apply the cartoon setting to an entire obj 
> (object). And so you are correct in trying to duplicate the nucleotide so you 
> can apply one setting to it, while allowing the other setting to display the 
> rest of them. But that doesn’t work either since the program will only allow 
> one display type at a time. There may be a complex way to override it but I 
> do not know it.
> 
> The way I have gotten around this in the past is to set up the entire object 
> the way you want it, then render it once with each setting.
> 
> Then open both of the resulting images in photoshop or similar program. Put 
> them both into one file as layers.
> 
> Then delete most of one of the files (say the top one) so only the single 
> nucleotide is left in the cartoon setting that you want in that layer. The 
> rest of the image will appear from the bottom layer.
> 
> Then you can flatten the image and save it. It’s fast and works great.
> 
> 
>> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
>> wrote:
>> 
>> Dear pymol-users,
>>  
>> I’m still learning how to use pymol to do basic things.
>> At present, I’m working with a nucleic acid molecule that is colored by 
>> sequence domains (each domain is a different objet). All the domains are 
>> displayed in the cartoon mode, with backbone as dumbbell and 
>> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
>> like to display only the first residue of one of the domains as 
>> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  
>> entirely (dumbbell + ribose stick + base ring) with a different color from 
>> the rest of the domain sequence.  The problem is that it does not work ! 
>>  
>> I tried to copy that nucleotide into a new objet to manipulate it 
>> independently but all the arguments I write in the command line do not apply 
>> to it, nothing is changing on the screen. The only thing that works is the 
>> menu on the right, use the objet line corresponding to this residue, display 
>> it entirely as sticks and then change the color of the sticks. But that’s 
>> not what I need!
>>  
>> Do you have any ideas how to display the desired nucleotide?
>>  
>> Many thanks in advance,
>>  
>> Maria
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
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PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Color residue in cartoon mode

[harold steinberg]

I believe that you can only apply the cartoon setting to an entire obj 
(object). And so you are correct in trying to duplicate the nucleotide so you 
can apply one setting to it, while allowing the other setting to display the 
rest of them. But that doesn’t work either since the program will only allow 
one display type at a time. There may be a complex way to override it but I do 
not know it.

The way I have gotten around this in the past is to set up the entire object 
the way you want it, then render it once with each setting.

Then open both of the resulting images in photoshop or similar program. Put 
them both into one file as layers.

Then delete most of one of the files (say the top one) so only the single 
nucleotide is left in the cartoon setting that you want in that layer. The rest 
of the image will appear from the bottom layer.

Then you can flatten the image and save it. It’s fast and works great.


> On Aug 2, 2016, at 9:41 AM, COSTA Maria  
> wrote:
> 
> Dear pymol-users,
>  
> I’m still learning how to use pymol to do basic things.
> At present, I’m working with a nucleic acid molecule that is colored by 
> sequence domains (each domain is a different objet). All the domains are 
> displayed in the cartoon mode, with backbone as dumbbell and 
> cartoon_ring_finder,0  (no nucleobases or riboses displayed). Now, I would 
> like to display only the first residue of one of the domains as 
> cartoon_ring_finder,2 (ring only for nucleobases) and then color it  entirely 
> (dumbbell + ribose stick + base ring) with a different color from the rest of 
> the domain sequence.  The problem is that it does not work ! 
>  
> I tried to copy that nucleotide into a new objet to manipulate it 
> independently but all the arguments I write in the command line do not apply 
> to it, nothing is changing on the screen. The only thing that works is the 
> menu on the right, use the objet line corresponding to this residue, display 
> it entirely as sticks and then change the color of the sticks. But that’s not 
> what I need!
>  
> Do you have any ideas how to display the desired nucleotide?
>  
> Many thanks in advance,
>  
> Maria
> --
> ___
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> 
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> 
H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] Color coded script

[Julian Heinrich]

Hi,

are you referring to the code examples? I think the coloring scheme is just
a source code syntax highlighting, where all strings for example are in
red, comments are in green, and functions are blue.

Cheers,
Julian

On Tue, Nov 10, 2015 at 3:15 PM,  wrote:

> Hi,
>
> In the PyMolWiki under simple scripting parts of the command lines are
> color coded(red, blue and green). What does that mean?
>
> cmd.extend(“doSimpleThing”,doSimpleThing)
>
>
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Re: [PyMOL] color an isosurface with a rainbow

[Sampson, Jared M.]

Hi H. Adam -

Try the http://pymolwiki.org/index.php/Distancetoatom script by Andreas 
Warnecke and use it to set b (or your own custom property in recent Incentive 
PyMOL versions) based on the distance from a point.

Hope that helps.

Cheers,
Jared

--
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Columbia University

On Mar 23, 2016, at 5:20 PM, harold steinberg 
> wrote:

I have a pdb ‘xyz1’ and create a mapA, then create a surfA.

set surface_quality, 1
alter all, b=50
alter all, q=1
set gaussian_resolution,5
map_new mapA, gaussian, 1, sele or pdb, 6
isosurface surfA, mapA

I can then color that surfA with any solid color.

How can one color the surfA with a rainbow affect that radiates out from the 
center, or similar.

This is easy to do with a protein (pdb) but I cannot get a ramp to work with a 
surf.


H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366

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Re: [PyMOL] color based on residue sequence

[Folmer Fredslund]

Hi Smith,

Have you tried reading in the wiki?

This page on advanced coloring (
http://pymolwiki.org/index.php/Advanced_Coloring) might help you to color
in a number of ways.
Your specific request could be handled by the util.chainbow command, which
is also available in the color menu of each object.

Best regards,
Folmer

2015-12-05 9:54 GMT+01:00 Smith Liu :

> Dear All,
>
> Is any way by pymol we color the protein based on residue sequence, for
> example from red starting resi 1 gradually to blue at residue 1000?
>
> Smith
>
>
>
>
>
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Re: [PyMOL] color a polypeptide continuously

[T. Nakane]

Hi,

In GUI, [Color]-[spectrum]-[rainbow].
 From command line,
  util.chainbow(name)

Best regards,

Takanori Nakane

On 2014-10-14 13:55, sunyeping wrote:
 Dear pymol user,
 
 Could you tell me how to color a polypeptide continuously from N- to
 C-terminal by continuous spectrum such as red to blue?
 
 Yeping Sun
 
 Institute of Microbiology, Chinese Academy of Sciences
 
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Re: [PyMOL] Color according to RMSD

[Tsjerk Wassenaar]

Hi Cedric,

The first part is numeric inaccuracy. You get all atomic rmsds in the range
of 0 - 1e-12 or so. Spectrum colors according to the extent of this range.
For the other one, note that the RMSD (mean sum of MSDs) is pretty low.
Usually, it's due to a few residues that don't align perfectly, giving a
pretty skewed RMSD distribution. Make sure to show lines or sticks for all
atoms that were used in the alignment. Especially when doing the alignment
on the whole protein and showing only the cartoon, you'll certainly miss
the atoms contributing most to the total RMSD.

Cheers,

Tsjerk

On Mon, Oct 6, 2014 at 10:01 PM, Cedric patrick.coss...@inbox.com wrote:

  Hi Tsjerk,

 Thank you-gorgeous idea.

 I have a quick question, I took a pdb, made a copy of it and called it
 1.pdb.

 Loaded 3CCD.pdb + 1.pdb (which are identical of course).

 Called your command, the structure appeared in all the colors of the
 rainbow.

 Now I load another structure with an overall RMSD of 0.4A to 3CCD, now
 when I call your aommand its only blue.

 Could you explain more? Also I didn't see the atomic rmsd being written to
 the file.

 I will admit my knowledge is very limited so I might be doing something
  wrong.

 Thank you


 -Original Message-
 *From:* tsje...@gmail.com
 *Sent:* Mon, 6 Oct 2014 20:53:41 +0200
 *To:* pymol-users@lists.sourceforge.net
 *Subject:* [PyMOL] Color according to RMSD


 Hey :)

 In response to an earlier question regarding coloring objects according to
 per residue RMSD, I wrote a small routine to color according to atom RMSD,
 after an alignment. Maybe it'll be of any use to someone...

 The script performs an alignment and then gets the corresponding atoms,
 for which the RMSDs are calculated. These are written to the b-factor
 fields of the atoms in both objects and the structures are colored.

 Any improvements are welcomed.

 Enjoy,

 Tsjerk


 ###

 import numpy

 from pymol import cmd


 def rmsd2b(selection1, selection2, cycles=5, scheme=rainbow):

 

 Align structures and write pairwise RMSDs to b-factor fields


 Author: Tsjerk A. Wassenaar

 


 cmd.align(selection1,selection2,cycles=int(cycles))


 # I would like to have a better way for this...

 # Find the element in the session list that corresponds to the object
 _align1

 # which is an object generated by cmd.align (likewise for _align2)

 # The list contains a number of things. The fifth element is the list
 of

 # IDs of atoms that are aligned to those in the other structure.

 aln1 = [i for i in cmd.get_session()[names] if i and i[0] ==
 _align1][0][5][0][1]

 aln2 = [i for i in cmd.get_session()[names] if i and i[0] ==
 _align2][0][5][0][1]


 m1 = numpy.array(cmd.get_model(selection1).get_coord_list())

 m2 = numpy.array(cmd.get_model(selection2).get_coord_list())


 # RMSD per atom in the alignment

 d = numpy.sqrt( ((m1[aln1,:]-m2[aln2,:])**2).sum(axis=1) )


 b1 = numpy.zeros(m1.shape[0])

 b2 = numpy.zeros(m2.shape[0])


 b1[aln1] = d

 b2[aln2] = d


 b1 = b1.tolist()

 b2 = b2.tolist()


 cmd.alter(selection1,b=b1.pop(0),space=locals())

 cmd.alter(selection2,b=b2.pop(0),space=locals())


 cmd.spectrum(b,scheme, (%s) or (%s)%(selection1, selection2))



 cmd.extend(rmsd2b,rmsd2b)



 --
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Re: [PyMOL] color each polymer chain differently

[Sampson, Jared]

Hi Chandan - Back in the lab today.  I took a look at the code I sent and 
realized that one can’t simply pass a tuple to cmd.color(), as it only accepts 
named colors, so you have to use cmd.set_color().

So here (below) is a modified, fleshed-out version of what I sent yesterday, 
with the protein components of the T. thermophilus ribosome asymmetric unit 
(110 chains) as an example.  For a larger number of colors, you would simply 
have to increase the ranges for i, j, and k in the loop that creates the RGB 
tuples.

Some of the colors turn out to be fairly similar (e.g. those differing by only 
one RGB component), so also maybe check out, e.g., this SO question and its 
answers for alternative approaches: 
http://stackoverflow.com/questions/470690/how-to-automatically-generate-n-distinct-colors.

Cheers,
Jared

###

from pymol import cmd
from random import shuffle

cmd.fetch(2wdk, async=0)
cmd.fetch(2wdl, async=0)
cmd.fetch(2wdm, async=0)
cmd.fetch(2wdn, async=0)

# remove non-polymer components so we can just view the cartoon
cmd.remove(all and not polymer)

# remove RNA chains to get a better view of individual protein chains
cmd.remove(chain A)

my_chains = []

for obj in cmd.get_names():
for ch in cmd.get_chains(obj):
my_chains.append((obj, ch))

print There are currently %s chains to be colored. % len(my_chains)

my_colors = []

# 5^3  100
for i in range (0, 5):
r = 0.25 * i
for j in range (0, 5):
g = 0.25 * j
for k in range (0, 5):
b = 0.25 * k
my_colors.append([r, g, b])

# randomize list (optional)
shuffle(my_colors)
print shuffled the colors

# name the colors
for i, tup in enumerate(my_colors):
cmd.set_color(mycolor_%s % i, %s % tup)
print set color mycolor_%s to %s % (i, tup)

# color your chains
for i, ch in enumerate(my_chains):
sel = %s and chain %s % (ch[0], ch[1])
color = mycolor_%s % i
color_tuple = my_colors[i]
print %s will be colored %s (%s) % (sel, color, color_tuple)
cmd.color(%s % color, sel)

###

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Mar 17, 2014, at 2:07 PM, Sampson, Jared 
jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org wrote:

Hi Chandan -

It seems like you're being limited by the 26 numbered colors in the util.cbc 
function. You could create your own randomized list of evenly-spaced colors, 
something like the following (untested, but should be approximately 
usable--sorry, I'm away from my computer today):

from pymol import cmd
from random import shuffle

my_colors = []

# 5^3  100
for i in range (0, 5):
   r = 0.25 * i
   for j in range (0, 5):
   g = 0.25 * j
   for k in range (0, 5):
   b = 0.25 * k
   my_colors.append([r, g, b])

# randomize list
shuffle(my_colors)

# color your chains
for x, c in enumerate(my_chain_list):
   cmd.color(my_colors[x], c)

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Kong Lab
NYU Medical Center
kong.med.nyu.eduhttp://kong.med.nyu.edu
212-263-7898

Sent from my iPhone

On Mar 17, 2014, at 8:37 AM, Thomas Holder thomas.hol...@schrodinger.com 
wrote:

Hi Chandan,

in Incentive PyMOL 1.6 you can use the spectrum command to color by chain (will 
be enumerated) or by residue number. http://pymolwiki.org/index.php/Spectrum

In open-source PyMOL, you could use the spectrumany script to color by residue 
number: http://pymolwiki.org/index.php/Spectrumany

Cheers,
Thomas

On 13 Mar 2014, at 03:19, Chandan Choudhury iitd...@gmail.com wrote:
On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis jwillis0...@gmail.com wrote:
I think...

What is happening is that the color command should take in a name like “color 
yellow, i. 1 or a CMYK color vector. When you are saying “color 1” it is just 
starting at the first index of CMYK which is black.

There is a command for your problem though. Just say util.color_chains() and it 
will color all individual chains a different color.

Thanks Jordon for the reply.

I tried using util.color_chains(). It colors differently upto chain no. 26. 
After 26 all the chains are of same color, as I donot have chain no after that.
Some utility which can color by residue number would be very useful.

Chandan

On Mar 12, 2014, at 11:15 PM, Chandan Choudhury iitd...@gmail.com wrote:

Dear PyMOL users,

I build 100 chains of polymer in a box. Residue number is different for every 
chain. Chain 1 hasresidue no. 1, chain 2 has residue no. 2 and so on. I want to 
color each chain differently.
So, I wrote a script which generates a pml file, and opening this pml file with 
PyMOL should color each chain differently.

##color.pml
load 128md_c.pdb
select 1, i. 1
color  1, i. 1
select 2, i. 2
color  2, i. 2
select 3, i. 3
color  3, i. 3
select 4, i. 4
color  4, i. 4
select 5, i. 5
color  5, i. 5
select 6, i. 6
color  6, i. 6
select 7, i. 7
...
...
color  125, i. 125
select 126, i. 126
color  126, i. 126
select 

Re: [PyMOL] color each polymer chain differently

[Thomas Holder]

Hi Chandan,

in Incentive PyMOL 1.6 you can use the spectrum command to color by chain (will 
be enumerated) or by residue number. http://pymolwiki.org/index.php/Spectrum

In open-source PyMOL, you could use the spectrumany script to color by residue 
number: http://pymolwiki.org/index.php/Spectrumany

Cheers,
  Thomas

On 13 Mar 2014, at 03:19, Chandan Choudhury iitd...@gmail.com wrote:
 On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis jwillis0...@gmail.com wrote:
 I think...
 
 What is happening is that the color command should take in a name like “color 
 yellow, i. 1 or a CMYK color vector. When you are saying “color 1” it is 
 just starting at the first index of CMYK which is black.
 
 There is a command for your problem though. Just say util.color_chains() and 
 it will color all individual chains a different color.
  
 Thanks Jordon for the reply. 
 
 I tried using util.color_chains(). It colors differently upto chain no. 26. 
 After 26 all the chains are of same color, as I donot have chain no after 
 that.
 Some utility which can color by residue number would be very useful.
 
 Chandan
 
 On Mar 12, 2014, at 11:15 PM, Chandan Choudhury iitd...@gmail.com wrote:
 
  Dear PyMOL users,
 
  I build 100 chains of polymer in a box. Residue number is different for 
  every chain. Chain 1 hasresidue no. 1, chain 2 has residue no. 2 and so on. 
  I want to color each chain differently.
  So, I wrote a script which generates a pml file, and opening this pml file 
  with PyMOL should color each chain differently.
 
  ##color.pml
  load 128md_c.pdb
  select 1, i. 1
  color  1, i. 1
  select 2, i. 2
  color  2, i. 2
  select 3, i. 3
  color  3, i. 3
  select 4, i. 4
  color  4, i. 4
  select 5, i. 5
  color  5, i. 5
  select 6, i. 6
  color  6, i. 6
  select 7, i. 7
  ...
  ...
  color  125, i. 125
  select 126, i. 126
  color  126, i. 126
  select 127, i. 127
  color  127, i. 127
  select 128, i. 128
  color  128, i. 128
 
  I have 128 chains.
 
  What I find that mostly green or black dominates the coloring.
  While displaying color by the numeric code, what is the maximum no, after 
  which the color repeats?
 
  Chandan
 
  --
  Chandan Kumar Choudhury
  National Chemical Laboratory, Pune
  India

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


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Re: [PyMOL] color each polymer chain differently

[Sampson, Jared]

Hi Chandan -

It seems like you're being limited by the 26 numbered colors in the util.cbc 
function. You could create your own randomized list of evenly-spaced colors, 
something like the following (untested, but should be approximately 
usable--sorry, I'm away from my computer today):

from pymol import cmd
from random import shuffle

my_colors = []

# 5^3  100
for i in range (0, 5):
r = 0.25 * i
for j in range (0, 5):
g = 0.25 * j
for k in range (0, 5):
b = 0.25 * k
my_colors.append([r, g, b])

# randomize list
shuffle(my_colors)

# color your chains
for x, c in enumerate(my_chain_list):
cmd.color(my_colors[x], c)

Hope that helps. 

Cheers,
Jared

--
Jared Sampson
Kong Lab
NYU Medical Center
kong.med.nyu.edu
212-263-7898

Sent from my iPhone

 On Mar 17, 2014, at 8:37 AM, Thomas Holder thomas.hol...@schrodinger.com 
 wrote:
 
 Hi Chandan,
 
 in Incentive PyMOL 1.6 you can use the spectrum command to color by chain 
 (will be enumerated) or by residue number. 
 http://pymolwiki.org/index.php/Spectrum
 
 In open-source PyMOL, you could use the spectrumany script to color by 
 residue number: http://pymolwiki.org/index.php/Spectrumany
 
 Cheers,
  Thomas
 
 On 13 Mar 2014, at 03:19, Chandan Choudhury iitd...@gmail.com wrote:
 On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis jwillis0...@gmail.com 
 wrote:
 I think...
 
 What is happening is that the color command should take in a name like 
 “color yellow, i. 1 or a CMYK color vector. When you are saying “color 1” 
 it is just starting at the first index of CMYK which is black.
 
 There is a command for your problem though. Just say util.color_chains() and 
 it will color all individual chains a different color.
 
 Thanks Jordon for the reply. 
 
 I tried using util.color_chains(). It colors differently upto chain no. 26. 
 After 26 all the chains are of same color, as I donot have chain no after 
 that.
 Some utility which can color by residue number would be very useful.
 
 Chandan
 
 On Mar 12, 2014, at 11:15 PM, Chandan Choudhury iitd...@gmail.com wrote:
 
 Dear PyMOL users,
 
 I build 100 chains of polymer in a box. Residue number is different for 
 every chain. Chain 1 hasresidue no. 1, chain 2 has residue no. 2 and so on. 
 I want to color each chain differently.
 So, I wrote a script which generates a pml file, and opening this pml file 
 with PyMOL should color each chain differently.
 
 ##color.pml
 load 128md_c.pdb
 select 1, i. 1
 color  1, i. 1
 select 2, i. 2
 color  2, i. 2
 select 3, i. 3
 color  3, i. 3
 select 4, i. 4
 color  4, i. 4
 select 5, i. 5
 color  5, i. 5
 select 6, i. 6
 color  6, i. 6
 select 7, i. 7
 ...
 ...
 color  125, i. 125
 select 126, i. 126
 color  126, i. 126
 select 127, i. 127
 color  127, i. 127
 select 128, i. 128
 color  128, i. 128
 
 I have 128 chains.
 
 What I find that mostly green or black dominates the coloring.
 While displaying color by the numeric code, what is the maximum no, after 
 which the color repeats?
 
 Chandan
 
 --
 Chandan Kumar Choudhury
 National Chemical Laboratory, Pune
 India
 
 -- 
 Thomas Holder
 PyMOL Developer
 Schrödinger, Inc.
 
 
 --
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Re: [PyMOL] color each polymer chain differently

[Chandan Choudhury]

On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis jwillis0...@gmail.comwrote:

 I think...

 What is happening is that the color command should take in a name like
 color yellow, i. 1 or a CMYK color vector. When you are saying color
 1 it is just starting at the first index of CMYK which is black.

 There is a command for your problem though. Just say util.color_chains()
 and it will color all individual chains a different color.


Thanks Jordon for the reply.

I tried using util.color_chains(). It colors differently upto chain no. 26.
After 26 all the chains are of same color, as I donot have chain no after
that.
Some utility which can color by residue number would be very useful.

Chandan




 On Mar 12, 2014, at 11:15 PM, Chandan Choudhury iitd...@gmail.com wrote:

 
  Dear PyMOL users,
 
  I build 100 chains of polymer in a box. Residue number is different for
 every chain. Chain 1 has residue no. 1, chain 2 has residue no. 2 and so
 on. I want to color each chain differently.
  So, I wrote a script which generates a pml file, and opening this pmlfile 
  with PyMOL should color each chain differently.
 
  ##color.pml
  load 128md_c.pdb
  select 1, i. 1
  color  1, i. 1
  select 2, i. 2
  color  2, i. 2
  select 3, i. 3
  color  3, i. 3
  select 4, i. 4
  color  4, i. 4
  select 5, i. 5
  color  5, i. 5
  select 6, i. 6
  color  6, i. 6
  select 7, i. 7
  ...
  ...
  color  125, i. 125
  select 126, i. 126
  color  126, i. 126
  select 127, i. 127
  color  127, i. 127
  select 128, i. 128
  color  128, i. 128
 
  I have 128 chains.
 
  What I find that mostly green or black dominates the coloring.
  While displaying color by the numeric code, what is the maximum no,
 after which the color repeats?
 
  Chandan
 
  --
  Chandan Kumar Choudhury
  National Chemical Laboratory, Pune
  India
 
 
 --
  Learn Graph Databases - Download FREE O'Reilly Book
  Graph Databases is the definitive new guide to graph databases and
 their
  applications. Written by three acclaimed leaders in the field,
  this first edition is now available. Download your free book today!
 
 http://p.sf.net/sfu/13534_NeoTech___
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-- 

--
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National Chemical Laboratory, Pune
India
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Re: [PyMOL] color each polymer chain differently

[Jordan Willis]

I think...

What is happening is that the color command should take in a name like “color 
yellow, i. 1 or a CMYK color vector. When you are saying “color 1” it is just 
starting at the first index of CMYK which is black.

There is a command for your problem though. Just say util.color_chains() and it 
will color all individual chains a different color. 



On Mar 12, 2014, at 11:15 PM, Chandan Choudhury iitd...@gmail.com wrote:

 
 Dear PyMOL users,
 
 I build 100 chains of polymer in a box. Residue number is different for every 
 chain. Chain 1 has residue no. 1, chain 2 has residue no. 2 and so on. I want 
 to color each chain differently.
 So, I wrote a script which generates a pml file, and opening this pml file 
 with PyMOL should color each chain differently.
 
 ##color.pml
 load 128md_c.pdb
 select 1, i. 1
 color  1, i. 1
 select 2, i. 2
 color  2, i. 2
 select 3, i. 3
 color  3, i. 3
 select 4, i. 4
 color  4, i. 4
 select 5, i. 5
 color  5, i. 5
 select 6, i. 6
 color  6, i. 6
 select 7, i. 7
 ...
 ...
 color  125, i. 125
 select 126, i. 126
 color  126, i. 126
 select 127, i. 127
 color  127, i. 127
 select 128, i. 128
 color  128, i. 128
 
 I have 128 chains.
 
 What I find that mostly green or black dominates the coloring. 
 While displaying color by the numeric code, what is the maximum no, after 
 which the color repeats?
 
 Chandan
 
 --
 Chandan Kumar Choudhury
 National Chemical Laboratory, Pune
 India
 
 --
 Learn Graph Databases - Download FREE O'Reilly Book
 Graph Databases is the definitive new guide to graph databases and their
 applications. Written by three acclaimed leaders in the field,
 this first edition is now available. Download your free book today!
 http://p.sf.net/sfu/13534_NeoTech___
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Re: [PyMOL] Color starting midway between adjacent chains

[I-Ji Jung]

Hi David,

Thanks. But what about between all chains? I mean, so between chains B and C 
and so on. I need a generic script that can be applied for any protein.

Thanks!

?? ??: David Hallmailto:li...@cowsandmilk.net
?? ??: ?2014?? ?3?? ?4??   ?2?:?57
?? ??: I-Ji Jungmailto:u5205...@anu.edu.au
??: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net

set_bond line_color, color_name, n. CA+CB

will color all bonds between CA and CB whatever color you put in as color_name

If you're doing sticks instead of lines, you should use

set_bond stick_color, color_name, n. CA+CB

-David




On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung 
u5205...@anu.edu.aumailto:u5205...@anu.edu.au wrote:
Hi everyone,

I have just started learning Pymol and PyMol seems to use a different colour 
convention than Molmol, i.e. the colour of a side chain starts half way between 
the CA and CB atoms (instead of starting at the CA). Do you know whether there 
would there be a way to start the side chain colour at the CA without changing 
the colour of the backbone?

Any help will be greatly appreciated!

Thank you.

I-Ji

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Re: [PyMOL] Color starting midway between adjacent chains

[David Hall]

set_bond line_color, color_name, n. CA+CB

will color all bonds between CA and CB whatever color you put in as
color_name

If you're doing sticks instead of lines, you should use

set_bond stick_color, color_name, n. CA+CB

-David




On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung u5205...@anu.edu.au wrote:

  Hi everyone,

  I have just started learning Pymol and PyMol seems to use a different
 colour convention than Molmol, i.e. the colour of a side chain starts half
 way between the CA and CB atoms (instead of starting at the CA). Do you
 know whether there would there be a way to start the side chain colour at
 the CA without changing the colour of the backbone?

  Any help will be greatly appreciated!

  Thank you.

  I-Ji


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 Subversion Kills Productivity. Get off Subversion  Make the Move to
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 the
 freedom to use Git, Perforce or both. Make the move to Perforce.

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Re: [PyMOL] Color by conservation

[Thomas Holder]

Hi Matzov,

the script assumed an old (incomplete) PyMOL API. I corrected the script, 
please download it again.

Cheers,
  Thomas

On 09 Jan 2014, at 16:27, Matzov Donna matzov.do...@weizmann.ac.il wrote:

 I'm trying to use the script that is available on pymolwiki for  colouring 
 residues according to conservation. It wasn't very clear to me so I tried to 
 do the given example:
 reinitialize
 import color_by_conservation
 
 # get some kinases
 fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 
 # turn on the sequence viewer
 set seq_view
 
 # align them into the algn object
 for x in cmd.get_names(): cmd.align(x, 3efw and c. A, object=algn)
 
 # color
 color_by_conservation aln=algn, as_putty=1
 
 everything went as it should but when it came to the last command pymol gave 
 me this error:  Bad or incorrectly specified alignment object
 
 How can I fix this problem?
 
 Thanks


-- 
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PyMOL Developer


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Re: [PyMOL] color change upon ray-tracing

[Thomas Holder]

Hi Vaheh,

there should be no color difference, apart from lighting effects. Ray
tracing always draws cylinders for mesh, real-time rendering supports
lines and cylinders.

Real-time rendering and ray tracing should be almost identical with
these settings:

PyMOL set use_shaders
PyMOL set mesh_as_cylinders
PyMOL unset mesh_radius
PyMOL unset ray_shadow

Notes:
 - mesh_radius only applies to ray tracing and only if not 0.0, use
   mesh_width to control for both rendering engines equally
 - mesh_as_cylinders only available with shaders

If you still don't get the same, please send screenshots.

Cheers,
  Thomas

Oganesyan, Vaheh wrote, On 09/03/13 19:47:
 PyMOLers,
 
 Upon ray-tracing PyMOL v1.6.0.0 (Linux 64 bit) changes the color and
 the mesh line width of the electron density maps. How can I disable
 this metamorphosis?
 
 Thank you.
 
 Vaheh

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Re: [PyMOL] Color changes during a morph

[Thomas Holder]

Hi Max,

you use a named color newcolor and change it's values at each
iteration, but all states refer to this same color. Before I show you
how to fix your script, could you give spectrum_states from the
PyMOLWiki a try? It's a script which does exactly what you want:

http://pymolwiki.org/index.php/Spectrum_states

PyMOL run spectrum_states.py
PyMOL spectrum_states resi 430-572, surface sphere, green magenta

Cheers,
  Thomas

Max NANAO wrote, On 03/25/13 21:27:
 Hi All,
 Can anyone tell me how I might change the colors of a specific 
 selection during the course of a rigimol generated morph?  I would like 
 one domain to go from purple to green, and have so far been unable to 
 figure out how to do it.  I tried coloring the different start/final 
 states before rigimol-ing but that did not work.  I have also tried to 
 script the state coloring, as described 
 here:http://www.pymolwiki.org/index.php/Color#Color_States_Individually. 
 The problem is that cmd.set(surface_color, newcolor, resi 
 430:572, a) for example, where a is the state, does not seem to work at 
 all.  i.e. the color is not changed.  The idea was to change the colors 
 as follows:
 
 states = 30
 for a in range(0,states):
  incr = 1.0/(states-1)
  r = 1.0-a*incr
  g = a*incr
  b = 1.0-a*incr
  col = [+str(r)+,+str(g)+,+str(b)+]
  cmd.set_color(newcolor,col)
  print COL state +str(a+1)+: +col
  cmd.set(surface_color, newcolor, resi 430:572, a)
  cmd.set(sphere_color,newcolor, resi 430:572, a)
  cmd.recolor()
 
 ugly, I know!  this is 64 bit pymol 1.5.0.6 eval for linux.  Thanks in 
 advance,
 
 Max

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Re: [PyMOL] color only certain states

[Jason Vertrees]

Hi Jordan,

Please see http://www.pymolwiki.org/index.php/Spectrum_states.

Cheers,

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Re: [PyMOL] Color states as rainbow

[Thomas Holder]

On 12/19/2011 11:20 PM, Jason Vertrees wrote:
 Cleaned up a little, this would make a nice simple addition to the
 PyMOLWiki script library.

I can do it, on the basis of spectrumany.

Cheers,
   Thomas

 Cheers,

 -- Jason

 On Mon, Dec 19, 2011 at 2:13 AM, Takanori Nakane
 t.nak...@mail.mfour.med.kyoto-u.ac.jp  wrote:
 Hi Jacob,

 The following command will make blue to purple spectrum.
   (please type in one line)

 for i in range(1 + cmd.count_states()): cmd.set(cartoon_color,
 0x%02x00ff % (i * 255 / (2 + cmd.count_states())), all, state=i)

 You can change spectrum by changing
0x%02x00ff % (i * 255 / (2 + cmd.count_states()))
 part.


 Best regards,

 Takanori Nakane

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Re: [PyMOL] Color states as rainbow

[Thomas Holder]

On 12/20/2011 11:49 AM, Thomas Holder wrote:
 On 12/19/2011 11:20 PM, Jason Vertrees wrote:
 Cleaned up a little, this would make a nice simple addition to the
 PyMOLWiki script library.

 I can do it, on the basis of spectrumany.

there it is:
http://pymolwiki.org/index.php/Spectrum_states

Cheers,
   Thomas

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Re: [PyMOL] Color states as rainbow

[Thomas Holder]

Hi Jacob,

I fixed the color_obj script in the wiki, it had a bug.

Btw. I like Tsjerk's suggestion best, using b-factors.

Cheers,
   Thomas

Jacob Keller wrote, On 12/19/11 03:38:
 Dear Pymol list,
 
 I have been trying to color the states in a morph by spectrum to try
 to show the motion in still form, using the following method:
 
 split_states foo, # after which I get the states as new objects as 
 expected
 color_obj(rainbow=1) # after which I get the following error message:
 
 Error: unknown type: 'models'
 
 Can someone help me out here--what's the error about? Or, still
 better, can you tell me the most efficient way to color the states by
 some color pattern (presumably I will just use the spectrum). This
 kind of thing should have been used in NMR or MD figures all the time,
 no?
 
 Thanks very much,
 
 Jacob Keller

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Re: [PyMOL] Color states as rainbow

[Thomas Holder]

Jacob Keller wrote, On 12/19/11 19:04:
 Yes, now it works perfectly--thanks very much! Also, did you see some
 advantage of doing the b-factor idea over your script, or just a good
 parallel strategy?

it's just a good parallel strategy. And is done with 2 lines instead of 
loading an extra script.

Cheers,
   Thomas

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Re: [PyMOL] Color states as rainbow

[Jacob Keller]

Yes, now it works perfectly--thanks very much! Also, did you see some
advantage of doing the b-factor idea over your script, or just a good
parallel strategy?

Jacob

On Mon, Dec 19, 2011 at 2:41 AM, Thomas Holder
spel...@users.sourceforge.net wrote:
 Hi Jacob,

 I fixed the color_obj script in the wiki, it had a bug.

 Btw. I like Tsjerk's suggestion best, using b-factors.

 Cheers,
  Thomas

 Jacob Keller wrote, On 12/19/11 03:38:

 Dear Pymol list,

 I have been trying to color the states in a morph by spectrum to try
 to show the motion in still form, using the following method:

 split_states foo,     # after which I get the states as new objects as
 expected
 color_obj(rainbow=1)     # after which I get the following error message:

 Error: unknown type: 'models'

 Can someone help me out here--what's the error about? Or, still
 better, can you tell me the most efficient way to color the states by
 some color pattern (presumably I will just use the spectrum). This
 kind of thing should have been used in NMR or MD figures all the time,
 no?

 Thanks very much,

 Jacob Keller


 --
 Thomas Holder
 MPI for Developmental Biology
 Spemannstr. 35
 D-72076 Tübingen



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Re: [PyMOL] Color states as rainbow

[Jason Vertrees]

Hi Jacob,

You cannot use the spectrum command across multiple states like that.
Your next best bet is to try:

set color, color_name, obj_name, state=X

For example,

set line_color, red, myProtein,  state=1
set line_color, orange, myProtein, state=2
set line_color, yellow, myProtein, state=3
...

Cheers,

-- Jason

On Sun, Dec 18, 2011 at 9:38 PM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
 type



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Re: [PyMOL] Color states as rainbow

[Tsjerk Wassenaar]

Hey :)

You could copy the state to the b-factor field:

fetch 1nmr, async=1
split_states 1nmr
for i in range(1,cmd.count_states()+1): cmd.alter(1nmr_%04d%i,b=%d%i)
delete 1nmr
spectrum b

Cheers,

Tsjerk

On Mon, Dec 19, 2011 at 7:38 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi Jacob,

 You cannot use the spectrum command across multiple states like that.
 Your next best bet is to try:

 set color, color_name, obj_name, state=X

 For example,

 set line_color, red, myProtein,  state=1
 set line_color, orange, myProtein, state=2
 set line_color, yellow, myProtein, state=3
 ...

 Cheers,

 -- Jason

 On Sun, Dec 18, 2011 at 9:38 PM, Jacob Keller
 j-kell...@fsm.northwestern.edu wrote:
 type



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 PyMOL Product Manager
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* Zernike Institute for Advanced Materials
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Re: [PyMOL] Color states as rainbow

[Takanori Nakane]

Hi Jacob,

The following command will make blue to purple spectrum.
  (please type in one line)

for i in range(1 + cmd.count_states()): cmd.set(cartoon_color, 
0x%02x00ff % (i * 255 / (2 + cmd.count_states())), all, state=i)

You can change spectrum by changing
   0x%02x00ff % (i * 255 / (2 + cmd.count_states()))
part.


Best regards,

Takanori Nakane

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Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

[Jason Vertrees]

Hi Hari,

 I am using svn pymol rev 3953 on a 64 bit Ubuntu box.
 I have a custom script that maps extent of conservation into the
 b-factor record of a pdb for visualization.

 I noticed a small feature in pymol

 My protein atoms in chain A have b-factors from 0 to 11 to indicate
 conservation extent , . The Heteroatoms , in this pdb also in  chain A
 have their ususal b-factors in the 60s.
 Now if I ask for the surface to be colored by bfactors spectrum for *.ca.

 Pymol echoes


  Spectrum: range ( 0.0 to 11.0).

We can quickly test the ranges to ensure PyMOL is acting appropriately:

withHET, withoutHET = [], []
iterate *, withHET.append(b)
iterate n. CA, withoutHET.append(b)

# print range w/HET

print min(withHET), max(withHET)

# print range wout/HET

print min(withoutHET), max(withoutHET)

and we can color by:

# color by spectrum

spectrum b, rainbow, n. CA


The problem I think you're having is that the colors don't expand to
the surface as you want.  I created a script awhile back to do just
this; see http://www.pymolwiki.org/index.php/Expand_To_Surface.

Please let us know if this helps.

Cheers,

-- Jason


 But the colors on the surface clearly also include the heteroatoms
 .which are all above 55 and in chain A.
 So the whole protein surface ends up blue since majority of values are below 
 11.

 I did get around this by removing the heteroatoms to a different chain
 . But it seems there is a discrepancy between what is echoed to the
 stdout and the color-range pymol displays on the screen in this
 instance.

 Hope this is not some setting that I am messing up on my side

 Thanks
 hari

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Re: [PyMOL] color surface by bfactor discrepancy between range reported on shell and range used

[hari jayaram]

Hi Jason
Thanks for your detailed reply and for pointers on the iterate command
for mapping the bfactors.

I think I understand whats going on and there was a fault in my
understanding i.e I was wrong.

Even though my script puts the conservation record as b-factor to all
atoms of any given residue .
If I say color surface by spectrum b-factors *.ca , pymol colors only
the calpha atoms by the range of b-factors ( 0 to 11). The remainder
non-calpha atom surfaces still have their default cpk based color.

I conveniently assumed the command  color surface by spectrum
b-factors *.ca would have colored all the residues in the surface
representation by the value of the b-factor for their corresponding
c-alpha atom.

In my case when I then used  color by bfactors ( all atoms in object
by implication). The hetatoms were getting dragged into the definition
for all atoms and skewing the range.

I was wrong in that the range was misreported.
Thanks for the clarification.
hari






On Tue, Jul 5, 2011 at 2:42 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
 Hi Hari,

 I am using svn pymol rev 3953 on a 64 bit Ubuntu box.
 I have a custom script that maps extent of conservation into the
 b-factor record of a pdb for visualization.

 I noticed a small feature in pymol

 My protein atoms in chain A have b-factors from 0 to 11 to indicate
 conservation extent , . The Heteroatoms , in this pdb also in  chain A
 have their ususal b-factors in the 60s.
 Now if I ask for the surface to be colored by bfactors spectrum for *.ca.

 Pymol echoes


  Spectrum: range ( 0.0 to 11.0).

 We can quickly test the ranges to ensure PyMOL is acting appropriately:

 withHET, withoutHET = [], []
 iterate *, withHET.append(b)
 iterate n. CA, withoutHET.append(b)

 # print range w/HET

 print min(withHET), max(withHET)

 # print range wout/HET

 print min(withoutHET), max(withoutHET)

 and we can color by:

 # color by spectrum

 spectrum b, rainbow, n. CA


 The problem I think you're having is that the colors don't expand to
 the surface as you want.  I created a script awhile back to do just
 this; see http://www.pymolwiki.org/index.php/Expand_To_Surface.

 Please let us know if this helps.

 Cheers,

 -- Jason


 But the colors on the surface clearly also include the heteroatoms
 .which are all above 55 and in chain A.
 So the whole protein surface ends up blue since majority of values are below 
 11.

 I did get around this by removing the heteroatoms to a different chain
 . But it seems there is a discrepancy between what is echoed to the
 stdout and the color-range pymol displays on the screen in this
 instance.

 Hope this is not some setting that I am messing up on my side

 Thanks
 hari

 --
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 --
 Jason Vertrees, PhD
 PyMOL Product Manager
 Schrodinger, LLC

 (e) jason.vertr...@schrodinger.com
 (o) +1 (603) 374-7120


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Re: [PyMOL] Color scale changed in APBS?

[Schubert, Carsten [PRDUS]]

Hi Wataru, 

in addition to what Jason mentioned: Have you tried to look at the
potential mapped on the solvent accessible surface and display the
molecular surface? If you display the potential like this the colors
will be much more muted, on the other hand this is the setting you will
find most often displayed in the literature.
Another option is to have a look at the charge distribution of your
molecule in the actual PQR file. The potential distribution is dependent
on the charging algorithm used. I would recommend using/looking into
PDQ2PQR, which is available from the APBS website and compare this to
the homegrown charging algorithm from PyMol or GRASP for that matter.

Hope I did not muddle the water too much

Carsten

 -Original Message-
 From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
 Sent: Monday, February 21, 2011 10:04 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Color scale changed in APBS?
 
 Dear PyMOL users:
 
 I recently used the APBS plugin (v1.3) to display the surface
potential
 of a protein. I noticed that the charged surfaces were much more
 lightly colored, compared with the surface colors I have calculated in
 the past (maybe a year ago?) on the same protein, using the same
 softwares. The default settings and the same range (-10 kT to 10 kT)
 were used in both cases. Has anyone experienced this?
 
 I would appreciate any help.
 
 Wataru
 
 

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Re: [PyMOL] Color scale changed in APBS?

[Michael Lerner]

Hi all,

On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] 
cschu...@its.jnj.com wrote:

 Hi Wataru,

 in addition to what Jason mentioned: Have you tried to look at the
 potential mapped on the solvent accessible surface and display the
 molecular surface? If you display the potential like this the colors
 will be much more muted, on the other hand this is the setting you will
 find most often displayed in the literature.


I think this is likely the case. Due to a lot of feedback, the plugin
defaults changed to showing the solvent accessible surface a while ago (see
the checkboxes in the Molecular Surface section of the Visualization panel).


 Another option is to have a look at the charge distribution of your
 molecule in the actual PQR file. The potential distribution is dependent
 on the charging algorithm used. I would recommend using/looking into
 PDQ2PQR, which is available from the APBS website and compare this to
 the homegrown charging algorithm from PyMol or GRASP for that matter.


Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting
that the current version of the plugin allows you to specify command line
arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying
out different force fields).

Cheers,

-Michael



 Hope I did not muddle the water too much

 Carsten

  -Original Message-
  From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
  Sent: Monday, February 21, 2011 10:04 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] Color scale changed in APBS?
 
  Dear PyMOL users:
 
  I recently used the APBS plugin (v1.3) to display the surface
 potential
  of a protein. I noticed that the charged surfaces were much more
  lightly colored, compared with the surface colors I have calculated in
  the past (maybe a year ago?) on the same protein, using the same
  softwares. The default settings and the same range (-10 kT to 10 kT)
  were used in both cases. Has anyone experienced this?
 
  I would appreciate any help.
 
  Wataru
 
 
 
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Re: [PyMOL] Color scale changed in APBS?

[Wataru Kagawa]

Here's a screenshot of the color scale. It appears to me that the red and blue 
colors are fainter than it should be. I tried using the ramp_new command as 
follows, but it is not working for me.

ramp_new ramp1, pymol-generated, [-10, 0, 10], [red, white, blue]

I would greatly appreciate any help.

inline: スクリーンショット（2011-02-23 14.37.54）.png
On 2011/02/22, at 23:23, Michael Lerner wrote:

 Hi all,
 
 On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] 
 cschu...@its.jnj.com wrote:
 Hi Wataru,
 
 in addition to what Jason mentioned: Have you tried to look at the
 potential mapped on the solvent accessible surface and display the
 molecular surface? If you display the potential like this the colors
 will be much more muted, on the other hand this is the setting you will
 find most often displayed in the literature.
 
 I think this is likely the case. Due to a lot of feedback, the plugin 
 defaults changed to showing the solvent accessible surface a while ago (see 
 the checkboxes in the Molecular Surface section of the Visualization panel).
  
 Another option is to have a look at the charge distribution of your
 molecule in the actual PQR file. The potential distribution is dependent
 on the charging algorithm used. I would recommend using/looking into
 PDQ2PQR, which is available from the APBS website and compare this to
 the homegrown charging algorithm from PyMol or GRASP for that matter.
 
 Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting 
 that the current version of the plugin allows you to specify command line 
 arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying 
 out different force fields).
 
 Cheers,
 
 -Michael
  
 
 Hope I did not muddle the water too much
 
 Carsten
 
  -Original Message-
  From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp]
  Sent: Monday, February 21, 2011 10:04 PM
  To: pymol-users@lists.sourceforge.net
  Subject: [PyMOL] Color scale changed in APBS?
 
  Dear PyMOL users:
 
  I recently used the APBS plugin (v1.3) to display the surface
 potential
  of a protein. I noticed that the charged surfaces were much more
  lightly colored, compared with the surface colors I have calculated in
  the past (maybe a year ago?) on the same protein, using the same
  softwares. The default settings and the same range (-10 kT to 10 kT)
  were used in both cases. Has anyone experienced this?
 
  I would appreciate any help.
 
  Wataru
 
 
 
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Re: [PyMOL] Color scale changed in APBS?

[Jason Vertrees]

Hi Wataru Kagawa,

The intensity of the colors depends on the values of the data and the
color ranges on the color ramp.  In fact, in editing mode,
CTRL-dragging can control the upper/lower values of the ramp,
effecting the coloring.  On top of that, you can assign colors to
different numerical values.

All that should matter in your case is that the actual values remain
the same.  Are they?  If not, have you investigated changes to the
algorithms or implementations?

Last, for more help on ramps, see http://www.pymolwiki.org/index.php/Ramp_New.

Cheers,

-- Jason

On Mon, Feb 21, 2011 at 10:04 PM, Wataru Kagawa wkag...@aoni.waseda.jp wrote:
 Dear PyMOL users:

 I recently used the APBS plugin (v1.3) to display the surface potential of a 
 protein. I noticed that the charged surfaces were much more lightly colored, 
 compared with the surface colors I have calculated in the past (maybe a year 
 ago?) on the same protein, using the same softwares. The default settings and 
 the same range (-10 kT to 10 kT) were used in both cases. Has anyone 
 experienced this?

 I would appreciate any help.

 Wataru


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Re: [PyMOL] color an isosurface

[Marius Retegan]

Hello
With help from Jason I've managed to solve my problem. As a result I've
updated the wiki page for the ramp_new command to include my particular case
(see bottom of the page)
http://pymolwiki.org/index.php/Ramp_New
Marius

On Mon, Jun 28, 2010 at 10:32 PM, Marius Retegan marius.s.rete...@gmail.com
 wrote:

 Hello,
 Take the following scenario. I have two cube files, the first one holds
 some values of a function (electron localization function),
 while in the second cube for each value in the first cube file i can have
 either one of the numbers from 0 to 6.
 After loading the first cube file in Pymol, I create an isosurface of a
 given value for the contour level, lets say 0.8 a.u.
 Next I want to color this isosurface based on the values in the second cube
 file, e.g. all points that have a value of 3 in the second cube
 should be colored red etc.
 Any ideas on how to accomplish this? If needed, I could provide the two
 cube files for a simple test case
 Thank you
 Marius


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Re: [PyMOL] color by element

[Gerebtzoff, Gregori]

What I personally do is:

cmd.color(grey50,all)
util.cnc(all)

So that my carbons have the color I wish (grey50), and other atoms are colored 
by element.

Best,

Greg


-Original Message-
From: David Hall [mailto:li...@cowsandmilk.net] 
Sent: Wednesday, February 10, 2010 1:45 AM
To: Ariel Talavera
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] color by element

First of all, there is:
color atomic
which will do all the colors and for whatever reason does green for carbons

Additionally, there's a general class of util.cba? where question mark
is replaced by one letter representing the color of carbon.  I've been
told by people that these are supposed to be internal commands and I
shouldn't use them, but I do and they've been there as long as I've
used pymol.

Currently, these are:
util.cbab for slate
util.cbag for green
util.cbam for magenta
util.cbap for purple
util.cbaw for white
util.cbac for cyan
util.cbak for pink
util.cbao for orange
util.cbas for salmon
util.cbay for yellow

You can see how these are implemented in
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup
if you want to make your own custom versions.

-David Hall

On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote:
 Hi Pymolers,

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?

 Thanks in advanced,

 Best,
 Ariel

 --
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 Center of Molecular Immunology
 calle 216 esq. A 15, Atabey, Playa
 Havana 11600, CUBA
 tel: (53-7) 271 7933, ext. 221
 fax: (53-7) 272 0644
 email: talav...@cim.sld.cu
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Re: [PyMOL] color by element

[Nathaniel Echols]

On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cu wrote:

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?


I don't think there's a single command that does this; I've always done
something like this:

color grey80, elem c
color white, elem h
color red, elem o
color blue, elem n
color orange, elem s

and so on (in python, these become 'cmd.color(grey80, elem c)', etc.).
 I just discovered that there is also a separate color name for each
element, e.g. color carbon, elem c will work, but the default coloring
scheme seems a bit wacky sometimes (carbon is green, etc.).  If there was a
convenient way to switch between available color sets (e.g. all of the
options available in the menus), that would be awesome.  Currently the
atom-name colors are hardcoded in C, unfortunately.

Nat
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Re: [PyMOL] color by element

[Michael Lerner]

have you tried:

import util
util.cbag
util.cbay
util.rainbow

etc?

after you type import util, you can type util. followed by a tab to
see the available commands.

On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols nathaniel.ech...@gmail.com
 wrote:

 On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera talav...@cim.sld.cuwrote:

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?


 I don't think there's a single command that does this; I've always done
 something like this:

 color grey80, elem c
 color white, elem h
 color red, elem o
 color blue, elem n
 color orange, elem s

 and so on (in python, these become 'cmd.color(grey80, elem c)', etc.).
  I just discovered that there is also a separate color name for each
 element, e.g. color carbon, elem c will work, but the default coloring
 scheme seems a bit wacky sometimes (carbon is green, etc.).  If there was a
 convenient way to switch between available color sets (e.g. all of the
 options available in the menus), that would be awesome.  Currently the
 atom-name colors are hardcoded in C, unfortunately.

 Nat


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Re: [PyMOL] color by element

[David Hall]

First of all, there is:
color atomic
which will do all the colors and for whatever reason does green for carbons

Additionally, there's a general class of util.cba? where question mark
is replaced by one letter representing the color of carbon.  I've been
told by people that these are supposed to be internal commands and I
shouldn't use them, but I do and they've been there as long as I've
used pymol.

Currently, these are:
util.cbab for slate
util.cbag for green
util.cbam for magenta
util.cbap for purple
util.cbaw for white
util.cbac for cyan
util.cbak for pink
util.cbao for orange
util.cbas for salmon
util.cbay for yellow

You can see how these are implemented in
http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol/modules/pymol/util.py?view=markup
if you want to make your own custom versions.

-David Hall

On Tue, Feb 9, 2010 at 5:46 PM, Ariel Talavera talav...@cim.sld.cu wrote:
 Hi Pymolers,

 How can I use the color by element (HNOS) function present in the GUI,
 in a script?

 Thanks in advanced,

 Best,
 Ariel

 --
 *
 Ariel Talavera Pérez, PhD
 Center of Molecular Immunology
 calle 216 esq. A 15, Atabey, Playa
 Havana 11600, CUBA
 tel: (53-7) 271 7933, ext. 221
 fax: (53-7) 272 0644
 email: talav...@cim.sld.cu
 *


 --
 SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
 Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
 http://p.sf.net/sfu/solaris-dev2dev
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Re: [PyMOL] color functionality for mac versions

[mnc2003]

Sorry but no this does not work.  I still get only 3 sliders; RBG, for 
both 1.0 and 1.2r2.  No luminocity etc that aere in the windows version. 
These sliders also seem to be absent for the linux version we run (1.0 I 
think).
Thanks Mark

 Mark ( indeed all Mac users)

 MacPyMOL can be launched in two flavors, based on the name of the
 executable:

 If the executabled is named MacPyMOL, PyMOL launches in the mode you're
 familiar with: a single-window Cocoa-based interface.

 If the executable is renamed PyMOLX11Hybrid, then PyMOL launches using
 the Tcl/Tk/X11-based, two-window interface you're familiar with from
 Windows and Linux. That's how you can get at the color slider you seek.

 Cheers,
 Warren

  -Original Message-
  From: mnc2...@co... [mailto:mnc2...@co...]
  Sent: Thursday, October 08, 2009 10:50 AM
  To: pymol-us...@li...
  Subject: [PyMOL] color functionality for mac versions

  Hi
  I was talking to a fellow student about coloring different molecules
 in an
  image for publication. And one reviewer suggested the 3 colors he was
  using were different of luminocity. He then showed me where to adjust
  this in the PC version. Setting  Colors... , and adjust or create
 new
  colors. I'm a mac user, and both macpymol and the hybrid version have
  only red, blue and green sliders in the modify colors menu. No Lum.
 slider
  or h/l/s boxes. I am missing something? I really like this
  functionality on the pc version.
  Thanks Mark
 
 
 
 
 
 
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Re: [PyMOL] color functionality for mac versions

[Warren DeLano]

Mark ( indeed all Mac users)

MacPyMOL can be launched in two flavors, based on the name of the
executable:

If the executabled is named MacPyMOL, PyMOL launches in the mode you're
familiar with:  a single-window Cocoa-based interface.

If the executable is renamed PyMOLX11Hybrid, then PyMOL launches using
the Tcl/Tk/X11-based, two-window interface you're familiar with from
Windows and Linux.  That's how you can get at the color slider you seek.

Cheers,
Warren

 -Original Message-
 From: mnc2...@columbia.edu [mailto:mnc2...@columbia.edu]
 Sent: Thursday, October 08, 2009 10:50 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] color functionality for mac versions
 
 Hi
 I was talking to a fellow student about coloring different molecules
in an
 image for publication.  And one reviewer suggested the 3 colors he was
 using were different of luminocity.  He then showed me where to adjust
 this in the PC version.  Setting  Colors... , and adjust or create
new
 colors.  I'm a mac user, and both macpymol and the hybrid version have
 only red, blue and green sliders in the modify colors menu. No Lum.
slider
 or h/l/s boxes.  I am missing something?  I really like this
 functionality on the pc version.
 Thanks Mark
 
 
 
 


--
 
 Come build with us! The BlackBerry(R) Developer Conference in SF, CA
 is the only developer event you need to attend this year. Jumpstart
your
 developing skills, take BlackBerry mobile applications to market and
stay
 ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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Re: [PyMOL] Color codes in mutagenesis wizard?

[DeLano Scientific]

Greetings Henning,

The visible disks  colors in the Mutagenesis Wizard indicate pairwise
overlap of atomic van der Waals radii.  The intent is to provide a
qualitative feedback regarding contacts and bumps.

Short green lines or small green disks are shown when atoms are almost in
contact or slightly overlapping.  Large red disks indicate signficant van
der Waals overlap.  Everything else lies between those extremes.

Cheers,
Warren

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 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net 
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
 Of Henning Stehr
 Sent: Tuesday, April 29, 2008 7:39 AM
 To: PyMOL-users@lists.sourceforge.net
 Cc: dinesh.soa...@ed.ac.uk
 Subject: [PyMOL] Color codes in mutagenesis wizard?
 
 Hi,
 
 I was asked the following question and couldn't find the 
 answer, can anyone help?
 
 When I mutate a buried small amino acid side-chain to a 
 larger one, it correctly reveals some clashes around that new 
 side-chain. I suppose the disk shaped clusters mean clashes. 
 Can someone please confirm this? I was wondering what the 
 colour of the disk shapes mean (red, green - do they refer to 
 atom type?), and does the variable size of the disk mean anything?
 
 Cheers,
 Henning
 
 ---
 Henning Stehr (Dipl. Ing.)
 Structural Proteomics Group
 Max-Planck-Institute for Molecular Genetics Ihnestrasse 63-73
 14195 Berlin, Germany
 ---
 
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Re: [PyMOL] Color residues by b-factor

[DeLano Scientific]

Tiago,

It's a little hard to tell from the code, but it appears to be the first
atom encountered in the traversal (the would usually be N).   The byres
option wasn't really intended for coloring by property, but rather, for
coloring by sequence (e.g. in a rainbow).

If were were to change the current behavior, would you agree that using the
numeric average of the value would make the most sense?

Cheers,
Warren

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Subscriber Support Services
mailto:del...@delsci.info
 

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net 
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
 Of Tiago Barros
 Sent: Saturday, February 23, 2008 11:43 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Color residues by b-factor
 
 Dear all,
 
 If I set byres=1 in the spectrum command, which value is 
 attributed to the residue? The average from the atoms in that 
 residue? The highest?  
 The lowest? I could not find the answer in the wiki or the 
 mailing list.
 
 Thanks in advance for your help.
 
 Tiago
 
 
 
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Re: [PyMOL] color in pymol

[DeLano Scientific]

 How can I use the color option in the Setting menu(Edit all) 
 to get more color in the cartoon.Thanx.

What do you mean by more color in the cartoon?  You set the cartoon color
independently using a command such as:

set cartoon_color, color-name

for example

set cartoon_color, red

Cheers,

DeLano Scientific LLC
Email Support Services 

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net 
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
 Of shivesh kumar
 Sent: Saturday, October 28, 2006 4:33 AM
 To: PyMOL-users@lists.sourceforge.net
 Subject: [PyMOL] color in pymol
 
 Dear all,
 How can I use the color option in the Setting menu(Edit all) 
 to get more color in the cartoon.Thanx.
 Shivesh
 
 shivesh
 
 
 shivesh
 
 
 
 Get your email and see which of your friends are online - 
 Right on the new Yahoo.com 
 http://us.rd.yahoo.com/evt=42973/*http://www.yahoo.com/preview  
 

Re: [PyMOL] color in pymol

[andreas]

Hey Shivesh,

you can get more color in your cartoons by coloring every residue
differently.

color red, i. 20
color blue, i. 21
color yellow, i. 22

Don't pay too much attention to the menus.  They're really just there so
traditional Mac and Windows users to get scared when they start using
PyMOL.  You will find that the command line does everything quicker and
easier.


Andreas


 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
 Of shivesh kumar
 Sent: Saturday, October 28, 2006 4:33 AM
 To: PyMOL-users@lists.sourceforge.net
 Subject: [PyMOL] color in pymol

 Dear all,
 How can I use the color option in the Setting menu(Edit all)
 to get more color in the cartoon.Thanx.
 Shivesh

 shivesh

RE: [PyMOL] color

[Warren DeLano]

Yes, it's called spectrum...but it looks like the docs don't exist yet.

PyMOLspectrum ?
Usage: spectrum [ expression [, palette [, selection [, minimum [, maximum
[, byres [, quiet ]]]

eg:

spectrum b
spectrum q
spectrum b, selection=my_obj
spectrum b, minimum=5, maximum=60
spectrum count, selection

spectrum b, TAB 

will show you the list of spectra names currently available

spectrum count, red_green

etc.

Cheers,
Warren



 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 s...@bu.edu
 Sent: Thursday, April 08, 2004 8:12 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] color
 
 Hi,
 
  
 
 I have a naïve question here. Is there any command line 
 equivalent to using the menu color the by spectrum (rainbows and etc)?
 
  
 
 Thanks!
 
  
 
 -shuhsien
 
 

RE: [PyMOL] color schemes

[Warren L. DeLano]

Kaushik,

set auto_color,off

before opening the first file.

   or

util.cbag

   afterwards.

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 Kaushik Raha
 Sent: Tuesday, June 10, 2003 7:27 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] color schemes
 
 Hi,
 
 I have been playing around with PyMOL 088 and I think the new features
 are absolutely great. However I notice that whenever I load a molecule
 in this version, it randomly (??) assigns it a coloring scheme for the
 representation.  I see the same thing in the roving detail feature
 (which I might add is an excellent feature that I had always wanted to
 see in a Molecular Graphics program). I liked the older version where
 every new molecule loaded had the same CHNOS color scheme. Is there a
 way to get back to the older way. I know I can revert back to it by a
 click of a mouse button. But thats still a click specially when I am
 visualizing a lot of molecules.
 
 thanks,
 Kaushik.
 
 
 
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Re: [PyMOL] color by ss

[Robert Campbell]

Hello,

* cami...@mrc-lmb.cam.ac.uk cami...@mrc-lmb.cam.ac.uk [2003-04-29 14:08] 
wrote:
 
 Hello Pymol community,
   I'm experiencing a problem when colouring a pdb by secondary 
 structure. The colour bleeds from the ends of helices and sheets into 
 loop.
 
 for example, if I were to
 
 color orange, a/49:52/
 color purple, a/53:55/
 color mred2, a/56:59/
 
 
 where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/  is 
 beta strand, I get bleed from the ends of the strand into the loop.

Try setting cartoon_discrete_colors to 'on' (or 1).

  set cartoon_discrete_colors, 1

or from the the Cartoon menu of the external GUI find Discrete
Colors as the last item in the menu.

Hope this helps,
Robert
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-633-2497
Kingston, ON K7L 3N6  Canada   http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2

Re: [PyMOL] color choices

[Lieven Buts]

Jianghai Zhu wrote:
 When I use color command, how many choices do I have for colors? Can I use
 direct rgb value?

The color command uses color names. You can define your own colors
with RGB values using the set_color command:

set_color whatever = [ 1.0, 0.3, 0.7 ]

After that you can use

color whatever, ...

-- 
Lieven Buts
Department of Ultrastructure

RE: [PyMOL] color by B-factor?

[Mathews, Irimpan]

Hi Cameron,

Please check the site below.

http://biophysics.med.jhmi.edu/rlc/work/pymol/color_b.py

regards,
Mathews


-Original Message-
From: Cameron Mura [mailto:cm...@mccammon.ucsd.edu]
Sent: Friday, February 28, 2003 12:48 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] color by B-factor?


Hello,
If possible, how does one color a PDB representation in PyMOL by the 
B-factor field??
Thanks!
Cameron

-- 
--
 Cameron Mura
 Urey Hall, Rm. 4234
 Department of Chemistry  Biochemistry
 University of California, San Diego
 La Jolla, CA 92093-0365
 Email: cm...@mccammon.ucsd.edu
 http://mccammon.ucsd.edu/~cmura
 Phone: 858.534.0956
 Fax:   858.534.7042
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Re: [PyMOL] color by B-factor?

[Daniel John Rigden]

Hi Cameron

To colour on a blue red scale, if your Bs go from 0 to 100 you can use the
following that Warren sent me one time

color br0,(all)
color br1,(b10)
color br2,(b20)
color br3,(b30)
color br4,(b40)
color br5,(b50)
color br6,(b60)
color br7,(b70)
color br8,(b80)
color br9,(b90)

Good luck

Daniel


+-+
|   Dr Daniel John Rigden |
| CENARGEN/EMBRAPA | e-mail: dan...@cenargen.embrapa.br   |
| Parque Estacao Biologica | http://www.cenargen.embrapa.br   |
| PqEB - Final - Av. W3 Norte  |  Phone:  +55 (61)448-4741|
| 70770-900, Brasilia-D.F.-BRAZIL  |  Fax:+55 (61)340-3658|
+-+



On Fri, 28 Feb 2003, Cameron Mura wrote:

 Hello,
 If possible, how does one color a PDB representation in PyMOL by the
 B-factor field??
 Thanks!
 Cameron

 --
 --
  Cameron Mura
  Urey Hall, Rm. 4234
  Department of Chemistry  Biochemistry
  University of California, San Diego
  La Jolla, CA 92093-0365
  Email: cm...@mccammon.ucsd.edu
  http://mccammon.ucsd.edu/~cmura
  Phone: 858.534.0956
  Fax:   858.534.7042
 --




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Re: [PyMOL] color by B-factor?

[Robert Campbell]

Hi Cameron

On 2003-02-28 12:48 you wrote:
 If possible, how does one color a PDB representation in PyMOL by the 
 B-factor field??

Yes, have a look at my color_b.py script in the PyMOL part of my web
site:

  http://biophysics.med.jhmi.edu/rlc/work/pymol

You need to do a run color_b.py first, to load the function and then 
use the color_b command to color your objects.  Please read the
beginning of the file for instructions.  Normally you would place this
file in the directory in which you run pymol.

Cheers,
Robert
-- 
Robert L. Campbell, Ph.D. r...@post.queensu.ca
Senior Research Associatephone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-633-2497
Kingston, ON K7L 3N6  Canada
PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5 F635 C0E2
 (out of date web site:http://biophysics.med.jhmi.edu/rlc)

RE: [PyMOL] Color plotting of electron density contours?

[DeLano, Warren]

Bill,

There has been some discussion of this desirable feature, but it doesn't 
currently exist.

Cheers,
Warren


 -Original Message-
 From: wgsc...@chemistry.ucsc.edu [mailto:wgsc...@chemistry.ucsc.edu]
 Sent: Tuesday, November 12, 2002 1:27 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Color plotting of electron density contours?
 
 
 Hi Folks:
 
 Is there a way to display a cross-section of electron density  
 (false)-color-coded for electron density?  In other words, I 
 would like 
 to produce a 2-D plot that looks like a contour map (eg: 
 output of CCP4 
 npo) but color-coded with respect to electron density.  A 
 continuum, if 
 possible, would actually be better than a series of contour lines.
 
 Has this by any chance been implemented in pymol or anywhere?
 
 Many thanks,
 
 Bill Scott
 
 
 
 William G. Scott
 
 Associate Professor
 Department of Chemistry and Biochemistry
 and The Center for the Molecular Biology of RNA
 Sinsheimer Laboratories
 University of California at Santa Cruz
 Santa Cruz, California 95064
 USA
 
 phone:  +1-831-459-5367 (office)
 +1-831-459-5292 (lab)
 fax: +1-831-4593139  (fax)
 
 
 
 
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RE: [PyMOL] color gradient

[DeLano, Warren]

Jeff,

It would take a little Python programming, but modules/pymol/util.py 
has the rainbow command which can be modified so as to give a more restricted 
gradient than the current rainbow.

usage:

load prot.pdb
util.rainbow(prot)

(or just select the rainbow option on the color pop-up menu on prot)

Cheers,
Warren


-- 
mailto:war...@sunesis.com 
Warren L. DeLano, Ph.D. 
Informatics Manager 
Sunesis Pharmaceuticals, Inc. 
341 Oyster Point Blvd. 
S. San Francisco, CA 94080 
(650)-266-3606  FAX:(650)-266-3501 
-Original Message-
From: jeff chao [mailto:jac...@scripps.edu]
Sent: Thursday, July 11, 2002 2:40 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] color gradient


i would like to make a color gradient (something like purple-cyan) from N to C.
is there an easy way to do this?  thanks, jeff

 
^^
Jeffrey A. Chao

The Scripps Research Institute  PHONE: (858)784-8743
Molecular Biology MB 33 FAX: (858)784-2903
10550 N. Torrey Pines Road  E-MAIL: jac...@scripps.edu
La Jolla, CA  92037  USA

^^
  

Re: [PyMOL] color association with state?

[Malcolm E Davis]

DeLano, Warren wrote:

 Sorry, this can't be done with the current versions -- colors are either 
 atomic or whole-object properties (with a couple of minor exceptions).

A follow-up newbie question:  Is it possible to map colors onto a surface on a 
per vertex basis?

Malcolm