Re: [PyMOL] Select crystal waters inside protein

Hi Martin & James,

is it just a coincident that you both ask almost the same question?

You could remove all water atoms with few protein contacts or with a 
small surface area. For example:

remove solvent beyond 3.5 of polymer
set dot_solvent
get_area solvent, load_b=1
remove solvent and b > 20

Hope that helps.

Cheers,
   Thomas

On 04/26/2012 10:55 AM, James Starlight wrote:
> Another question- I have my protein.pdb with some inserted crystall
> waters within protein interiour as well as water surrounded of my
> protein. I want to remove only sorrounding water but prevent internal
> water ( wich could be functional relevant ).
>
> How I could to select such surrounded water ( e.g via some cutoff
> radius relative my protein etc) wich I'd like to remove further ?

On 04/25/2012 05:34 PM, Martin Hediger wrote:
> In a crystal structure, there are usually a number of relevant crystal
> waters, as well as water molecules on the surface. In our approach, we
> model the protein structure within a dielectric continuum, so surface
> water molecules are not required (to save computer time). However,
> waters in the interior should remain in our model. How could we discard
> the surface waters while keeping the internal waters?

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen