Dear Lu Zuokun,
There are several methods you can use to locate these problem residues.
Here are 3:
a) manually step through your PDB file in coot (good practice anyway, this
is fundamentally what we as crystallographers should be doing when we are
model building)
b) identify waters with close contacts as has been detailed earlier in this
discussion
c) run a round of refinement -
if you use buster, it will fail to start and the output files
contain full details of all of the close atoms/residues, then you can go
through and edit/delete as required in coot (or in a text editor).
if you use phenix or refmac to refine, and if the refinement
doesn't fail (again, details in the logs will tell you why), then the atoms
should refine away from each other during positional refinement. Then on
your next round of model building when you step through the entire
structure in coot, you'll see this.
I've done this a few times due to careless/over-exuberant use of keyboard
shortcuts in coot. It's not too onerous to identify and fix these problems,
though!
Regards
Isaac
On 30 October 2014 12:14, Tim Gruene <[email protected]> wrote:
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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" <[email protected]> 写道：
> >
> >
> > On Wed, Oct 29, 2014 at 8:53 PM, luzuok <[email protected]> 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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