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 <kru...@ukzn.ac.za> Date: Saturday, 27 November 2021 at 5:05 pm To: Ali Saad Kusay <akus8...@uni.sydney.edu.au> Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net> 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" <kru...@ukzn.ac.za> 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 UKZN email disclaimer: The contents of this e-mail may contain personal information, and/or privileged information, and/or confidential information. The information contained herein is therefore only meant for consumption by the recipient mentioned and for the purpose as specified in the body of the e-mail. Should you receive this e-mail in error kindly inform the sender of such by responding to the sender via a response e-mail and thereafter please delete the original e-mail received as well as the response e-mail. The University of KwaZulu-Natal e-mail platform is meant for business purposes (of the University) only and the University therefore does not accept any liability whatsoever that may arise from instances where such platform is utilised for personal reasons. Any views or opinions expressed in this e-mail represent those of the author and may not necessarily be binding on the University. The author of the e-mail may also not bind the University in any manner that may be construed from the contents of the e-mail unless such sender has been granted the requisite authority to do so by the University. _______________________________________________ PyMOL-users mailing list Archives: https://protect-au.mimecast.com/s/G7JzCXLW2mUXKGn89c6nIX_?domain=mail-archive.com<https://protect-au.mimecast.com/s/pyYTCVARKgCxym6OVtJhaUc?domain=protect-za.mimecast.com> Unsubscribe: https://protect-au.mimecast.com/s/ZungCYW8NocLlg3n9iGRDSs?domain=sourceforge.net<https://protect-au.mimecast.com/s/jj3uCXLW2mUXKjRplu9gQzs?domain=protect-za.mimecast.com>
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