Re: [PyMOL] Color change of different domain

[mailto:mohammad.goda...@gmail.com] Sent: 16 August 2018 20:58 To: j...@ebi.ac.uk Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Color change of different domain 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 co

Re: [PyMOL] Color change of different domain

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

Re: [PyMOL] Color change of different domain

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

Re: [PyMOL] Color backbone amide nitrogen

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)

Re: [PyMOL] Color bar for volume?

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%

Re: [PyMOL] Color residue in cartoon mode

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

Re: [PyMOL] Color residue in cartoon mode

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

Re: [PyMOL] Color residue in cartoon mode

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

Re: [PyMOL] Color coded script

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 si

Re: [PyMOL] color an isosurface with a rainbow

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 -- Jared Sampson Columbia University On Mar 23

Re: [PyMOL] color based on residue sequence

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 obje

Re: [PyMOL] color a polypeptide continuously

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

Re: [PyMOL] Color according to RMSD

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,

Re: [PyMOL] color each polymer chain differently

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 protei

Re: [PyMOL] color each polymer chain differently

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

Re: [PyMOL] color each polymer chain differently

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/Spectrum

Re: [PyMOL] color each polymer chain differently

On Thu, Mar 13, 2014 at 10:21 AM, Jordan Willis 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

Re: [PyMOL] color each polymer chain differently

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() an

Re: [PyMOL] Color starting midway between adjacent chains

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 Hall ?? ??: ?2014?? ?3?? ?4?? ?2?:?57 ?? ??: I-Ji Jung

Re: [PyMOL] Color starting midway between adjacent chains

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 wrote: > Hi everyo

Re: [PyMOL] Color by conservation

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 wrote: > I'm trying to use the script that is available on pymolwiki for colouring > residues according to conservation. It

Re: [PyMOL] color change upon ray-tracing

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

Re: [PyMOL] Color changes during a morph

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/ind

Re: [PyMOL] color only certain states

Hi Jordan, Please see http://www.pymolwiki.org/index.php/Spectrum_states. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Thi

Re: [PyMOL] Color states as rainbow

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

Re: [PyMOL] Color states as rainbow

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 > wrote: >> Hi

Re: [PyMOL] Color states as rainbow

Cleaned up a little, this would make a nice simple addition to the PyMOLWiki script library. Cheers, -- Jason On Mon, Dec 19, 2011 at 2:13 AM, Takanori Nakane wrote: > Hi Jacob, > > The following command will make blue to purple spectrum. >  (please type in one line) > > for i in range(1 + cmd.

Re: [PyMOL] Color states as rainbow

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 wrote: > Hi Jacob, > > I fixed the color_obj script in the wiki, it had a bug. > > B

Re: [PyMOL] Color states as rainbow

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 scri

Re: [PyMOL] Color states as rainbow

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

Re: [PyMOL] Color states as rainbow

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 / (

Re: [PyMOL] Color states as rainbow

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 wrote: > Hi Jacob, > > You cannot use th

Re: [PyMOL] Color states as rainbow

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 ...

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

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

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

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 > conserv

Re: [PyMOL] Color scale changed in APBS?

Thank you for the suggestion. I've looked at the gamma setting, but it was 1.0, so the washed out effect is not because of the gamma setting. I've noticed that raytracing removes the washed out effect of the scale bar, but not so much of the protein surface color. Is there by any chance that the

Re: [PyMOL] Color scale changed in APBS?

Wataru, just a thought: Have you looked into the gamma setting in pymol? Setting gamma to 4.0 from 1.0 and raytracing reproduces the washed out effect. > -Original Message- > From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp] > Sent: Tuesday, February 22, 2011 7:19 PM > To: Michael Ler

Re: [PyMOL] Color scale changed in APBS?

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

Re: [PyMOL] Color scale changed in APBS?

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 potent

Re: [PyMOL] Color scale changed in APBS?

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 o

Re: [PyMOL] Color scale changed in APBS?

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 val

Re: [PyMOL] color an isosurface

Hi all, To clearly state what Marius is intimating: we can calculate any property of atoms and color the surface based on that property. His example uses ELF. We created the surface from one map, and colored it from another. While his application is very specific, PyMOL will allow you to color

Re: [PyMOL] color an isosurface

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 wrote: > Hello, > Ta

Re: [PyMOL] color by element

, 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? whe

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 b

Re: [PyMOL] color by element

have you tried: import util util.cbag util.cbay util.rainbow etc? after you type "import util", you can type "util." followed by a to see the available commands. On Tue, Feb 9, 2010 at 6:09 PM, Nathaniel Echols wrote: > On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera wrote: > >> How can I use

Re: [PyMOL] color by element

On Tue, Feb 9, 2010 at 2:46 PM, Ariel Talavera 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

Re: [PyMOL] color functionality for mac versions

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 launc

Re: [PyMOL] color functionality for mac versions

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 launc

Re: [PyMOL] Color codes in mutagenesis wizard?

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 slig

Re: [PyMOL] Color residues by b-factor

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 curr

Re: [PyMOL] color in pymol

s > -Original Message- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of andr...@biochem.utah.edu > Sent: Saturday, October 28, 2006 8:01 AM > To: 'shivesh kumar'; pymol-users@lists.sourceforge.net

Re: [PyMOL] color in pymol

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.

Re: [PyMOL] color in pymol

> 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,

Re: [PyMOL] color individual residues on a surface?

On Jul 23, 2004, at 4:16 PM, Chris Larkin wrote: hi michael- such a figure should be no problem, could you send me an example of what you're ending up with and maybe I can figure out your problem. chris Hi Chris, thanks for your willingness to help me troubleshoot: I may have been too hast

RE: [PyMOL] color

-Original Message- From: Warren DeLano [mailto:war...@delanoscientific.com] Sent: Thursday, April 08, 2004 12:27 PM To: s...@bu.edu; pymol-users@lists.sourceforge.net Subject: RE: [PyMOL] color Yes, it's called spectrum...but it looks like the docs don't exist yet. PyMOL>spe

RE: [PyMOL] color

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

RE: [PyMOL] color schemes

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- > Fro

RE: [PyMOL] color by grasp phi map potential?

The minimal sequence is shown here: load molecule.pdb, mol-object load grasp-map.phi, map-object ramp_new ramp-name, map-object show surface, mol-object set surface_color, ramp-name, mol-object -- For example: load molb.pdb load molb.phi, e_pot ramp_new e_lvl, e_pot show surface, molb set sur

Re: [PyMOL] color by ss

Hello, * 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/

Re: [PyMOL] color choices

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 co

Re: [PyMOL] color by B-factor?

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

Re: [PyMOL] color by B-factor?

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,(b>10) color br2,(b>20) color br3,(b>30) color br4,(b>40) color br5,(b>50) color br6,(b>60) color br7,(b>70) color br8,(b>80) color br9,(b>90) Go

RE: [PyMOL] color by B-factor?

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] colo

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

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

RE: [PyMOL] color by partial charge? (electrostatics)

Mark, Coloring by partial charge should work fine, provided that you supply partial charges to PyMOL...which isn't trivial. You could either assign them using the 'alter' command after loading a PDB or SDF file, or you could convert your molecule into a Chemical Python "model" object, assig

RE: [PyMOL] color gradient

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

RE: [PyMOL] color association with state?

> From: Malcolm E Davis [mailto:malcolm.da...@bms.com] > > A follow-up newbie question: Is it possible to map colors > onto a surface on a per vertex basis? Not yet, but that functionality is planned for sometime this year in order to enable painting of surfaces in a non-atomic fashion. For n

Re: [PyMOL] color association with state?

"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

RE: [PyMOL] color association with state?

> From: Byron DeLaBarre [mailto:by...@slac.stanford.edu] > Subject: [PyMOL] color association with state? > Do any pymolers out there know how to associate the color of > a single object > with its state? Sorry, this can't be done with the current versions -- colors are either atomic or whole-o