Re: [PyMOL] Color by conservation

[Thomas H. <tho...@sc...>]

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 <mat...@we...> wrote:

> 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 sequence viewer
> set seq_view
> 
> # align them into the "algn" object
> for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
> 
> # color
> color_by_conservation aln=algn, as_putty=1
> 
> everything went as it should but when it came to the last command pymol gave me this error:  "Bad or incorrectly specified alignment object"
> 
> How can I fix this problem?
> 
> Thanks


-- 
Thomas Holder
PyMOL Developer