[Chimera-users] How to delete range of solvent molecules

Elaine Meng meng at cgl.ucsf.edu
Wed May 22 16:07:18 PDT 2013


Hi Andrés,
There are many possible ways. One way would be to select only the water molecules you want to keep and then use the command:

delete solvent & ~sel

(delete solvent that is not selected).  You can show the command line using the Favorites menu, and select with the mouse as described here
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect>

...or with a command, for example

select :445.A,480.A

Since you only want to keep a few and delete many, this approach is probably easier than selecting or listing all the ones you wanted to delete.
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 May 21, 2013, at 8:57 AM, felipe vasquez wrote:

> Hi, 
> I am trying to prepare a protein structure for docking, and I want to keep just one or a couple of water molecules. How can I do achieve this goal, deleting the rest of solvent molecules? Thanks in advance.
> Best regards,
> Andrés Felipe Vásquez J., MSc.
> Grupo de Fisiología Molecular
> Instituto Nacional de Salud
> Avenida calle 26 No. 51-20 - Zona 6 CAN
> Bogotá, D.C., Colombia 




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