All:
I second Mark's points
1. that "electrons/A3" doesn't make any sense in the context of an r.m.s.d. level, i.e. the "electrons/A3" should be deleted. Moreover, I would note the inconsistency in nomenclature between that line and the previous one where "with B factor greater than: ____ A^2", where the caret (circumflex) is used to indicate that the 2 should superscripted.
3. No way exists to specify the map used, although presumably it is using the first 2Fo-Fc map in the list and the list of suspect water molecules is consonant with that assumption.
However, I have never seen the dialog freeze COOT.
Additionally, for this dialog to be more useful:
4. it should use the PDB definition of a distant contact, which is not any protein atom, but rather a protein atom with a potential to form a hydrogen bond. To compensate for this deficiency, I search for water molecules whose closest contact is > 3.2 A. However, I have seen water molecules that are >~ 3.35 A from a hydrogen bonding atom sometimes move to farther than 3.5 A away on a subsequent round of refinement.
5. it should pay attention to LINK records and exclude water molecules whose closest contact is less than specified, but included in a LINK record.
Steven
>-----Original Message-----
>From: Mailing list for users of COOT Crystallographic Software
>[mailto:[log in to unmask]] On Behalf Of Mark A Saper
>Sent: Thursday, February 06, 2014 9:02 PM
>To: [log in to unmask]
>Subject: Problem with Check waters dialog
>
>I've never understood the Check Waters Dialog.
>
>1. The line "with map r.m.s.d. level less than 1.0 electrons/A3" doesn't
>make sense. Shouldn't it be with map density less than 1.0 sigma above
>mean (or r.m.s.) density value of the map?
>
>2. Sometimes the dialog causes the program to freeze, yet there are no
>informatory messages on the console.
>
>3. I would just like to find the waters that have 2Fo-Fc density less
>than 1 sigma. Also I don't think there is a place to specify the map
>name.
>
>-Mark
>
>_______________________________________________
>Mark A. Saper, Ph.D.
>Associate Professor of Biological Chemistry, U-M Medical School
>3040 Chemistry Building | [log in to unmask] | +1 (734) 764-3353
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