Hi Thomas,

I wounder to know what corrections should I add to the below selection in case of multi state object

remove solvent beyond 3.5 of polymer

e.g I'm working with the MD trajectory saved in PDB format. I've decided to deleate all solvent from all 100 frames simultaneously but the above command works fine only in case of 1 state object .


2012/4/26 Thomas Holder <speleo3@users.sourceforge.net>
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.


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