Re: [PyMOL] Complement or Inverse Selection in Pymol

[Ali S. K. <aku...@un...>]

Hi Gret,

No worries,

In regards to the selection: “resi 25 and object”

Its more so to ensure that you don’t accidently select “resi 25” from multiple chains or objects

Like if you load two pdb files into PyMOL (say obj01 and obj02) and both have a resi 25, then resi 25 from both objects will be selected if you don’t include the object in the selection.

On the other hand, If you:

select chA, resi 25 and obj01

Then the chA selection will only contain resi 25 from obj01 and ignore obj02.

Its more of a note about selections that you might already be familiar with

Cheers,

Ali

From: Gert Kruger <KR...@uk...>
Date: Saturday, 27 November 2021 at 5:05 pm
To: Ali Saad Kusay <aku...@un...>
Cc: "pym...@li..." <pym...@li...>
Subject: Re: [PyMOL] Complement or Inverse Selection in Pymol

Dear Ali,

Many thanks for your kind and very helpfull reply!  One question:

You wrote:  "Doing something like resi 25 and object is safer".

Do you mean: select chA, resi 25

And will that reflect as follows in my requirement:

select other_waters, br. (resn WAT beyond 5 of chA, resi 25)

Best wishes
Gert Kruger

On Fri, 2021-11-26 at 15:09 +0000, Ali Saad Kusay wrote:
Hi Gert,

These selection commands will generate a selection object called "other_waters "

See https://pymolwiki.org/index.php/Selection_Algebra<https://protect-au.mimecast.com/s/h0hkCQnMBZfkPgpznSPf8vp?domain=protect-za.mimecast.com>

You can do:
select other_waters, br. (resn WAT and not sele) # after you make the selection in your email
or
select other_waters, br. (resn WAT beyond 5 of resi 25)

A few notes:
1) you need to select by residue otherwise your selection will yield incomplete water molecules i.e. waters with 1-2 atoms in the selection as opposed to all 3 atoms. To do this use "br."
2) Be careful of selections like resi 25 since if you have multiple chains or objects with "resi 25", all will be included in the selection. Doing something like resi 25 and object is safer, object is the name in the object list in PyMOL

To remove the unwanted water atoms, do:

remove other_waters

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate & Pharmacist
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

On 27/11/21, 1:57 am, "Gert Kruger" <KR...@uk...> wrote:

Dear All,

Apologies for my ignorance. I need to know which solvent molecules are
in the active site of an enzyme (HIV-PR). I use "tleap" in Amber to
create a solvent waterbox in and around the enzyme.

I found the following command that seems to find the Water molecules in
the active site:

> sele resn WAT within 5 sele resi 25

(ASP25 is in the active site).

Now I want to remove ALL other water/solvent molecules (those that are
not selected).

Is there a method to achieve a complement or inverse selection (to
hightlight ALL other watermolecules that are not currently selected?)

I am able save the selection, but that is a bit more tedious.

Question: Is there an easy way in Pymol to achieve a "complement" or
"inverse" selection of waters in a solvent box?
Thanks alot and best wishes
Gert Kruger

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