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Dear Lu Zuokun,
it may appear tedious, but for a good quality model you should check
every position and decide yourself what to place there. Automation
will not replace your chemical understanding.
Regards,
Tim
On 10/30/2014 10:56 AM, luzuok wrote:
> Dear Nat,
>
>
> But if there are other solvent molecules, such as Mg2+, SO4-,,,,,,
> in the same position.
>
>
> How can this problem be solved?
>
>
> Lu Zuokun
>
>
>
>
>
> -- 卢作焜 南开大学新生物站A202
>
> 在 2014-10-30 12:57:31,"Nat Echols" <[log in to unmask]> 写道:
>
>
> On Wed, Oct 29, 2014 at 8:53 PM, luzuok <[log in to unmask]> wrote:
>
> I think it is better for COOT to solve this issue.
>
>
> Coot already can be used to solve this issue - I think the
> automation is somewhat lacking, but it's vastly preferable to
> anything involving a text editor or shell commands.
>
>
> 1. Load molecule and electron density maps in Coot
>
> 2. From the "Validate" menu, select "Check/Delete waters..."
>
> 3. Just select for waters with very close distances, for example
> 0.2Å; I've attached a screenshot of what it should look like.
>
> 4. This will give you a list of overlapping waters - then you just
> need to delete one of each pair. (It doesn't matter which one -
> the waters will be renumbered later anyway.)
>
>
> Alternately, you can set "Action" to "Delete", which is much less
> effort, but that will delete both copies. If you are just going to
> run a program (or Coot function) to place more waters automatically
> (my preference), this won't matter, but if they're atoms you really
> care about, you should delete them manually.
>
>
>
> -Nat
>
>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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