Hi Martin,

2012/10/4 Martin Hediger <ma.hed@bluewin.ch>
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

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?

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,

Further feedback would be greatly appreciated.

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?

Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!

Folmer Fredslund