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Dear Lu,
To be quite honest, before running refinement, I still use a simple program to add and delete waters based on electron density and distance criteria,
which I wrote a long time ago in the dark ages of Vax computers and Evans & Sutherland graphics when automatic water update did not exist. This program will guaranteed solve your problem. It is written in fortran with no dependencies, so it should be easy
to get it running and I will be happy to send it with instructions so that even a GUI addict can use it.
However, I am very surprised that a modern programs like Phenix would just crash and do not have options to clean-up the waters before starting
refinement.
Best regards,
Herman
Von: luzuok [mailto:[log in to unmask]]
Gesendet: Freitag, 31. Oktober 2014 01:33
An: Schreuder, Herman R&D/DE
Cc: [log in to unmask]
Betreff: Re:[ccp4bb] AW: [ccp4bb] water at the same exactly position
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, "" <[log in to unmask]> 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:[log in to unmask]]
Im Auftrag von luzuok
Gesendet: Donnerstag, 30. Oktober 2014 04:54
An: [log in to unmask]
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" <[log in to unmask]> 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 [[log in to unmask]] de la part de luzuok [[log in to unmask]]
>Envoyé : mercredi 29 octobre 2014 13:08
>À : [log in to unmask]
>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
>