Re: [PyMOL] electrostatic potential as cartoon?

[Thomas Holder]

Erratum: Of course I meant "solvent accessible", not "excluded".

On 05 Jan 2017, at 09:52, Thomas Holder  wrote:

> Hi Vincent,
> 
> Coloring the cartoon with a color ramp is not possible unfortunately. 
> Incentive PyMOL since version 1.8 can color ribbon by ramp, if that helps.
> 
> However, electrostatic potential locally probed along the backbone will not 
> be very meaningful. Typically you would look at electrostatics beyond the 
> solvent excluded surface, which you'll get in PyMOL either with 
> surface_solvent=1 or with surface_ramp_above_mode=1, 
> seehttps://pymolwiki.org/index.php/surface_ramp_above_mode
> 
> To visualize the distribution of charged or polar residues with cartoon, your 
> "flimsy" color scheme by residue type seems quite valid.
> 
> Cheers,
>  Thomas
> 
> On 04 Jan 2017, at 11:05, vincent Chaptal  wrote:
> 
>> Hi everyone, 
>> 
>> is there a way to color by electrostatic potential but display the structure 
>> as cartoon? 
>> 
>> a workaround could be :
>> color white, molecule
>> color red, resn asp+glu+thr+ser  etc..
>> color blue, resn arg+lys
>> 
>> ... but this seems rather flimsy. 
>> 
>> Thank you and best wishes for the new year. 
>> Vincent
>> 
>> 
>> -- 
>> Vincent Chaptal, PhD
>> Institut de Biologie et Chimie des Protéines
>> Drug Resistance and Membrane Proteins Laboratory
>> 7 passage du Vercors 
>> 69007 LYON
>> FRANCE
>> +33 4 37 65 29 01
>> http://www.ibcp.fr

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] electrostatic potential as cartoon?

[Thomas Holder]

Hi Vincent,

Coloring the cartoon with a color ramp is not possible unfortunately. Incentive 
PyMOL since version 1.8 can color ribbon by ramp, if that helps.

However, electrostatic potential locally probed along the backbone will not be 
very meaningful. Typically you would look at electrostatics beyond the solvent 
excluded surface, which you'll get in PyMOL either with surface_solvent=1 or 
with surface_ramp_above_mode=1, see 
https://pymolwiki.org/index.php/surface_ramp_above_mode

To visualize the distribution of charged or polar residues with cartoon, your 
"flimsy" color scheme by residue type seems quite valid.

Cheers,
  Thomas

On 04 Jan 2017, at 11:05, vincent Chaptal  wrote:

> Hi everyone, 
> 
> is there a way to color by electrostatic potential but display the structure 
> as cartoon? 
> 
> a workaround could be :
> color white, molecule
> color red, resn asp+glu+thr+ser  etc..
> color blue, resn arg+lys
> 
> ... but this seems rather flimsy. 
> 
> Thank you and best wishes for the new year. 
> Vincent
> 
>  
> -- 
> Vincent Chaptal, PhD
> Institut de Biologie et Chimie des Protéines
> Drug Resistance and Membrane Proteins Laboratory
> 7 passage du Vercors 
> 69007 LYON
> FRANCE
> +33 4 37 65 29 01
> http://www.ibcp.fr

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] electrostatic potential as cartoon?

[Jed Goldstone]

Vincent,
You could use data2bfactor.py and then "spectrum b" to color residues in 
cartoon settings.
https://pymolwiki.org/index.php/Color
(data2bfactor from Robert Campbell's script repository:
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Jed


On 1/4/2017 11:05 AM, vincent Chaptal wrote:
> Hi everyone,
>
> is there a way to color by electrostatic potential but display the
> structure as cartoon?
>
> a workaround could be :
> color white, molecule
> color red, resn asp+glu+thr+ser  etc..
> color blue, resn arg+lys
>
> ... but this seems rather flimsy.
>
> Thank you and best wishes for the new year.
> Vincent
>
>
> --
>
> Vincent Chaptal, PhD
>
> Institut de Biologie et Chimie des Protéines
>
> Drug Resistance and Membrane Proteins Laboratory
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.ibcp.fr
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>
>
>
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>

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[PyMOL] electrostatic potential as cartoon?

[vincent Chaptal]

Hi everyone,

is there a way to color by electrostatic potential but display the 
structure as cartoon?


a workaround could be :
color white, molecule
color red, resn asp+glu+thr+ser  etc..
color blue, resn arg+lys

... but this seems rather flimsy.

Thank you and best wishes for the new year.
Vincent


--

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug Resistance and Membrane Proteins Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr


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