Dear Herman,
If there are duplicate atoms in my PDB, Phenix refine GUI will post error
and crash (Sorry I haven't tried other refinement program). And there is no
.geo output file if program crash.
Phenix refine thought them as nonbonded atoms with distance equal to 0.
Because there are clash_guard parameter with nonbonded_distance_threshold =
0.5 .
I think I may try to turn of the clash_guard parameter.
Best Regards!
Lu Zuokun
--
卢作焜
南开大学新生物站A202
At 2014-10-30 22:26:00, "" <herman.schreu...@sanofi.com> wrote:
Dear Lu,
I don’t see your problem. Why don’t you use the automatic water update option,
present in most modern refinement programs, as Pavel suggested? This should
take care of your problem.
Of course, having premium, 1st class hand-picked waters is still the gold
standard, but I don’t believe the automatic waters are significantly worse. If
you go down the list of waters, you start with fully occupied, well-defined
waters, via partially occupied, less well-defined waters to overlapping,
partially occupied waters, disordered carbohydrate chains, buffer components,
cryo protectants and whatever else might have been present in your
crystallization solution. I do not check my waters, but I carefully check any
residual difference density. In the end it will be a subjective decision,
either by yourself, or by an automatic procedure based on a number of cut-off
criteria, whether or not to fit a water in some blob of density.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von luzuok
Gesendet: Donnerstag, 30. Oktober 2014 04:54
An:CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] water at the same exactly position
Dear Nicolas,
It is really time-consuming! Philip told me to run the structure on PDB
validation server. It will post error if there is duplicate molecules. Then I
can directly find them on a text editor.
I think it is better for COOT to solve this issue.
Best reagards!
Lu zuokun
--
卢作焜
南开大学新生物站A202
在 2014-10-29 22:29:35，"FOOS Nicolas" <nicolas.f...@synchrotron-soleil.fr> 写道：
>Dear Lu,
>
>one simple solution is to remove the water molecules with text editor for
>example. It depend of how-many times you have multiply water molecules and if
>your model have several or more water molecules.
>In coot you can remove it graphically, but according to my knowledge not
>automatically, and it maybe time consuming.
>
>Hope to help
>Nicolas
>
>________________________________________
>De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de luzuok
>[luzuo...@126.com]
>Envoyé : mercredi 29 octobre 2014 13:08
>À : CCP4BB@JISCMAIL.AC.UK
>Objet : [ccp4bb] water at the same exactly position
>
>Dear all,
> I found that there are some water molecules in my pdb that share the same
> position. This maybe cause by merging molecules in coot. It seems that I have
> mereged water molecules into my protein for more than one time.
>Does anyone tell me how to fix this problem?
>
>Best regards!
>Lu Zuokun
>
>
>
>
>--
>卢作焜
>南开大学新生物站A202
>
