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 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):

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

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

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

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, > >

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

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

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 to

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

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:

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

Re: [PyMOL] color each polymer chain differently

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.

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()

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 Hallmailto:li...@cowsandmilk.net ?? ??: ?2014?? ?3?? ?4?? ?2?:?57 ?? ??: I-Ji

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 u5205...@anu.edu.au

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 matzov.do...@weizmann.ac.il wrote: I'm trying to use the script that is available on pymolwiki for colouring residues

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

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:

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 --

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

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

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

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

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 spel...@users.sourceforge.net wrote: Hi Jacob, I fixed the color_obj script in

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 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 jason.vertr...@schrodinger.com wrote: Hi

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 / (2 +

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 conservation

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

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

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 potential

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

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

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

Re: [PyMOL] color by element

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

Re: [PyMOL] color by element

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

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 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

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

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 launched

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

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

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

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 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

RE: [PyMOL] color

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,

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-

Re: [PyMOL] color by ss

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

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 color

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]

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,(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

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 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 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?

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