Re: [PyMOL] Scripting coloring method via own calculations

[Tsjerk Wassenaar]

Hey :)

Just as sidenote, the spectrum command takes arbitrary color schemes. Just
combine colors separated by underscores. Also fun in combination with
set_color :)

Cheers,

Tsjerk

On Feb 14, 2017 5:46 PM, "Robert Campbell" 
wrote:

Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will
do that for you.  You create a file with whitespace-separated columns
(spaces and/or tabs) in which each line contains:

chain resi resn name data

(i.e. chain, residue number, residue name, atom name and value to be
applied to the B-factor column).

The number can also be applied to the occupancy column instead if you want
to keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour
each atom according to the data value.  My color_b.py script has a few more
options than the spectrum command, including the ability to define a custom
colour gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir  wrote:

> Hello,
>
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
>
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
>
> Best,
>
> Peleg




--
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] Scripting coloring method via own calculations

[Robert Campbell]

Hello Peleg,

I think there are other possibilities, but my data2bfactor.py script will do 
that for you.  You create a file with whitespace-separated columns (spaces 
and/or tabs) in which each line contains:

chain resi resn name data 

(i.e. chain, residue number, residue name, atom name and value to be applied to 
the B-factor column).

The number can also be applied to the occupancy column instead if you want to 
keep the B-factor intact.

Then you can use the spectrum command or my color_b.py script to colour each 
atom according to the data value.  My color_b.py script has a few more options 
than the spectrum command, including the ability to define a custom colour 
gradient scheme.

You can find my scripts here:

http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

Cheers,
Rob

On Tue, 2017-02-14 17:12  +0100,  Peleg Bar-Sapir  wrote:

> Hello,
> 
> I wish to write a script that will take the molecule loaded in PyMol,
> and color the molecule according to values I will calculate using the
> molecules' parameters (in the end there will be one floating number
> per atom). Then, I would like to display that using surface mode.
> 
> Could anyone direct me to a way of doing that? I saw scripts coloring
> by atom type, but I'm not sure how to apply it for a molecule already
> loaded in PyMol.
> 
> Best,
> 
> Peleg




-- 
Robert L. Campbell, Ph.D.
Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences, Botterell Hall Rm 644
Queen's University, Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
  http://pldserver1.biochem.queensu.ca/~rlc

--
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engaging tech sites, SlashDot.org! http://sdm.link/slashdot
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[PyMOL] Scripting coloring method via own calculations

[Peleg Bar-Sapir]

Hello,

I wish to write a script that will take the molecule loaded in PyMol, and
color the molecule according to values I will calculate using the
molecules' parameters (in the end there will be one floating number per
atom). Then, I would like to display that using surface mode.

Could anyone direct me to a way of doing that? I saw scripts coloring by
atom type, but I'm not sure how to apply it for a molecule already loaded
in PyMol.

Best,

Peleg
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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