[PyMOL] Color by Atom from CLI (not PyMol's GUI)

Hi. I'm working with PyMol's Python API from the terminal. I would like to color the molecules in my session by atom using the command util.cbac(). I want them in cyan because I'm deleting the two molecules involved and reopening the files with those molecules several times inside a loop. My first

[PyMOL] color by index

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[PyMOL] Color by index

hello everyone! I am trying to color an explicit distribution by color (say blue to red) pls help me with the command color by index thanks! Vertika Gautam Research Assistant Drug Design and Development Research Group (DDDRG) Department of Chemistry, Faculty of Science University of Malaya

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

iology > > > > > > 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

Re: [PyMOL] Color change of different domain

://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 fir

[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 ba

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)

[PyMOL] Color backbone amide nitrogen

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 backbo

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%

[PyMOL] Color bar for volume?

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. -

[PyMOL] color ramp for colorbyrmsd

Hi Pymolers I would like some help regarding a spectrum bar. I have generated an homology model of a structure and I wanted to compare to the template, to achieve this I have used the colorbyrmsd script https://pymolwiki.org/index.php/ColorByRMSD It works great but I would like to generate a

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

[PyMOL] Color residue in cartoon mode

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_fi

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

[PyMOL] Color coded script

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)-- Find and fix application performance issues fa

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

[PyMOL] color an isosurface with a rainbow

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 rainbo

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

[PyMOL] color based on residue sequence

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-- Go from Idea to Many App Stores Faster with Intel(R) XDK Giv

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

[PyMOL] color a polypeptide continuously

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 -- Comprehensive

Re: [PyMOL] Color according to RMSD

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:* [Py

[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 whic

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

[PyMOL] color each polymer chain differently

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 shoul

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

[PyMOL] Color starting midway between adjacent chains

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 c

[PyMOL] Color by conservation

Hi all, Does anyone know where can I find a legend for the colors I get when applying the "color by conservation" module? Thanks, Donna -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Bu

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

[PyMOL] Color by conservation

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 sequen

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

[PyMOL] color change upon ray-tracing

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 To the extent this electronic communication or any of its attachments contain information that is no

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

[PyMOL] Color changes during a morph

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

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

[PyMOL] color only certain states

Hello, What I want to do seems so simple, I just can't find the documentation. Would anyone know how to just change the colors of only certain states when they are appended to the same object? For instance I have a simulation that shows atoms moving all over the place for states 1-300 and a ni

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 ...

[PyMOL] Color states as rainbow

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 mess

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

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

Hi, 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

Re: [PyMOL] Color scale changed in APBS?

Cc: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net >> Subject: [PyMOL] Color scale changed in APBS? >> >> Thank you very much for the suggestions. >> I have been mapping the potential on the solvent accessible surface >> and displaying the molecular su

Re: [PyMOL] Color scale changed in APBS?

To: Michael Lerner > Cc: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net > Subject: [PyMOL] Color scale changed in APBS? > > Thank you very much for the suggestions. > I have been mapping the potential on the solvent accessible surface > and displaying the molecular

Re: [PyMOL] Color scale changed in APBS?

t; > 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: [PyMO

[PyMOL] Color scale changed in APBS?

gt; > 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

Re: [PyMOL] Color scale changed in APBS?

taru 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 dis

Re: [PyMOL] Color scale changed in APBS?

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

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

[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 soft

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

[PyMOL] color an isosurface

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 c

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

[PyMOL] color by element

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

Re: [PyMOL] color functionality for mac versions

; 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 s

Re: [PyMOL] color functionality for mac versions

sday, 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

[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 col

[PyMOL] Color By RMSD -- New Script

Hello List, A new PyMol script for coloring two objects by mutual RMS Deviation is now available on the PyMol wiki: http://pymolwiki.org/index.php/ColorByRMSD Hope some of you will find it useful... Many thanks to Jason Vertrees for help with turning the initial proof-of-principle into useful c

[PyMOL] Color menus off?

Hi all, I just upgraded to the pymol 1.2b2. The install works perfectly etc. I have a strange phenomenon though, all the colors in the menu on the right side of the graphics windows have disappeared as well as the colors in the sequence panel. Any hint what it might be? I have not change my con

Re: [PyMOL] Color codes in mutagenesis wizard?

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, >

[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

Re: [PyMOL] Color residues by b-factor

> [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,

[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

[PyMOL] color on color

I have two subunits surface-painted with the color ramp from Protskin http://www.mcgnmr.ca/ProtSkin/intro/index.html I would like to color one of the subunits so that it can be distinguished, but without hiding the color ramp. Suggestions? Dave -- David N. Garboczi, PhD Phone: 301-496-4773 I

[PyMOL] color key using ConSurf

Hi all, I am using ConSurf server to calculate the consurf scores and trying to generate pictures in Pymol. I followed their instructions and everything worked fine. I just have one question. Does anyone know how to generate the color key in Pymol? The color key image on the website d

[PyMOL] Color by residue type

Hi, I would like to color residues by their type using (more or less) standard colors (e.g. like in sPDBv). Could not find a command in Pymol that would do that. Did I miss it? Is there a way to avoid doing this one residue type at the time? Thanks for you help,

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

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 in pymol

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 > > ___

[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

[PyMOL] color gradient

Perhaps someone knows a better way to do this - I'm trying to make a color gradient on a surface based on distance from some selection using code like this: for a in range (1:100):\ cmd.set_color("mycolor",[1,1,a/100])\ cmd.color mycolor, my_surface within ((-1/100*a)+1) of my_selection Now I

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

[PyMOL] color individual residues on a surface?

Hi PyMOL'ers I'm trying to figure out how to do something that looks like the following figure: http://www.uvm.edu/~mbovee/structures/surface.png It seems any individual residues I color always map onto the cartoon ribbon representation rather than onto the surface representation. Is this c

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

half 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 > >

[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

[PyMOL] color by b-factor

Hello all, I have colored and rendered a pdb file in pymol according to the b-factor. What i would like to do is to also show a vertical/horizontal color bar indiacting the b-factor variation. is there a way to do this in pymol? Thank you, Regards, Smita

RE: [PyMOL] color schemes

age- > 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 playi

[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

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

day, June 07, 2003 3:13 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] color by grasp phi map potential? > > Well, this question is probably directed straight to Warren unless > someone's found it in the code or I've missed an obvious button. > > Main quest

[PyMOL] color by grasp phi map potential?

Well, this question is probably directed straight to Warren unless someone's found it in the code or I've missed an obvious button. Main question: I wrote out a GRASP potential map and read it in to PyMOL with no complaints. How do I then go about applying it to a surface (i.e. coloring the

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