-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFUUiuJUxlJ7aRr7hoRAp+GAJ0f7y+JtPptqADxkFQIoQjOXMuI6QCgj0UB CtBP+UbvdJ7b5pFfUOtp3KA= =yOAl -----END PGP SIGNATURE-----
