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Hi,

from what you explain, the main issue I see here is that the model building program does not treat water simply as density peaks, and so removes them (waters) if necessary to build a protein chain instead.

Otherwise, it's probably a good idea in general to fill in all unmodeled places with some placeholders like water, or probably isolated N atoms would work even better (if I recall correctly).

Pavel.

On 9/7/09 6:18 AM, crystallogrphy wrote:

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Hi, Pavel: The problem here is that autobuild placed waters into the densities where they are the N-terminal residues. Without the waters here, autobuild will build residues, not waters, to decrease R and Rfree with less model bias. Now with water picking, autobuild does not build more residues, just water. I still do not know why 'place_waters=False' cannot work. Tom has not given me the answer yet. On Mon, Sep 7, 2009 at 1:45 AM, Pavel Afonine mailto:[email protected]> wrote: Hi, I hope Tom gives you the answer about how to stop water picking in autobuild. From my side, I'm wondering why it bothers you (I'm not saying

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incompleteness may make the map ugly even for relatively well

defined places.

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Pavel. On 9/6/09 7:38 AM, crystallogrphy wrote:

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Hi, I am building a model against a 2.1A data set using phenix.autobuild. Right now Rfree is about 35%. I do not want to

Hi Qun, With your command you need to add one more keyword to get rid of all the waters: place_waters_in_combine=False I'm sorry that doesn't happen automatically if you say place_waters=False ...I will make that happen in the future. Note however that these waters should not interfere with building...as waters are always deleted prior to building model. I note also that your command does not add new residues; it only adjusts the ones that are there. To build new model add: rebuild_in_place=False All the best, -Tom T that not working option is good)? Why don't you consider those waters as a tool for improving your map? You are free to remove any of them them later on. This can be viewed as a prototype of what ARP/wARP does, or other "density growing" techniques... In your case you just temporarily place waters where the model is still absent, and when you build those missing places just consider waters as density peaks (I hope model building programs assume waters as just density peaks and remove waters if they are on the macromolecule's way). On the other hand, model pick water in this stage because I see denisty at N-terminal of my model which need to build more residues. However, the program still picks water even after I say 'place_waters=False'. Does anyone know why?

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phenix.autobuild data=exptl_fobs_phases_freeR_flags.mtz model=AutoBuild_run_4_/overall_best-090905a.pdb seq_file=../ztb-sd.seq refinement.place_waters=False refinement.refine_with_ncs=True nproc=2 ------------------------------------------------------------------------

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