Re: [PyMOL] Select crystal waters inside protein

[Folmer F. <fo...@gm...>]

Hi Martin,


2012/10/4 Martin Hediger <ma...@bl...>

> Dear PyMOL Users
> I'm trying to remove water molecules from a crystal structure which are
> on the crystal surface while preserving the ones within the crystal
> interior.
>
> What I do is:
>
> select waters, resn HOH
> # cmd.select("waters", "(waters extend 1)", enable=1)
> get_area waters, load_b=1
> remove waters and b>20
>
> This only works partially because of some waters, only the oxygen atom
> is removed, while of others only one of the hydrogens is removed (some
> waters are completely removed which is good). It does not make a
> difference if I include the commented command above.
>

You might want to read up on the selection algebra of PyMOL (
http://www.pymolwiki.org/index.php/Selection_Algebra) which is quite
powerfull.

You can use the "by residue" selection to select the entire residue that
fits you description, so in your case

remove byres waters and b>20

Will remove every residues within your selection waters, where at least one
atom has a b factor of more than 20. (and of course now you have altered
the b factor according to the calculated surface area)



Also, what does "load_b=1" mean?
>
>
http://www.pymolwiki.org/index.php/Get_Area
It is explained in the last example (3)
"load_b=1" will put the value of the surface area into the b factor column.


Hope that helps!

Best regards,
Folmer




> Further feedback would be greatly appreciated.
> Martin
>
>
>
>
>
> On 26.04.12 14:46, Thomas Holder wrote:
> > 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?
> >
>
>
>
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-- 
Folmer Fredslund