[Chimera-users] Structure editing

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 2 13:17:54 PDT 2014


Hi George,
(1) alternate locations: yes, you can delete all but the highest occupancy conformation using Dock Prep (in the menu under Tools… Structure Editing).  Turn off all of the other options, assuming you don’t want to do the other things.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html>

(2) deleting all waters except the selected ones: yes, you can easily do that with a command.  Select the waters you want to keep, then use command:

delete :hoh  &  ~  sel
(or...)
delete solvent  &  ~  sel

…”&” is logical AND (intersection), “~” is logical NOT, “sel” means the current selection.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 2, 2014, at 10:37 AM, George Tzotzos <gtzotzos at me.com> wrote:

> I’m dealing with a X-ray model in which some of the residues are shown in two conformations. Is it possible to edit the structure keeping the higher occupancy conformation ONLY?
> 
> Another question is whether it is possible to delete all waters but the selected ones (e.g. HOH molecules in the binding pocket that are conserved). I’ve been doing this manually using an editor and I wonder if there is better way of doing this.
> 
> Thanks in advance for your advice
> Regards
> George




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