Hi Martin,
2012/10/4 Martin Hediger
> 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 exte
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 wat
Hi James,
the "beyond" operator yields true only if the considered atom pair
distance is beyond the threshold in ALL states. To remove atoms which
are beyond threshold in ANY state, try this:
python
for i in range(cmd.count_states()):
cmd.select('tmp', 'solvent beyond 5 of polymer', state=
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
c
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
Dear List
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
