[phenixbb] Fw: Strange behaviour of phenix.maps fill_missing_f_obs
pafonine at lbl.gov
Thu Feb 5 17:34:06 PST 2015
in recent Phenix versions we replaced "kick map" option with a
generalized (and more sophisticated) concept that we call FEM - Feature
Enhanced Map. The paper is scheduled to appear in Acta D:
Meanwhile you can read through the set of pages that explain the concept
and show examples:
Let me know if you have questions!
On 2/5/15 1:12 AM, Tristan Croll wrote:
> My previous email was hung up in moderation due to my attaching a jpeg
> that tripped the size limit. In any case, I've done a bit more testing
> and the problem doesn't actually originate in the fill_missing_f_obs,
> but in the kicked map algorithm. If, as per the attached parameter
> file, I have a kicked map in the to-do list, every map past that point
> is garbled (the kicked map itself appears fine). Set kicked to False,
> and all maps come out looking normal.
> I should also note that the sharpening_b_factor parameter seems
> inverted from the normal convention: a negative value gives smoothing
> rather than sharpening.
> *From:* Tristan Croll
> *Sent:* Thursday, 5 February 2015 3:47 PM
> *To:* phenixbb at phenix-online.org
> *Subject:* Strange behaviour of phenix.maps fill_missing_f_obs
> I'm working on a package that makes scripted calls to phenix.refine to
> generate a series of ccp4 formatted maps, and have run into an odd
> problem. Using the attached parameter file I get a series of perfectly
> normal-looking maps, except in the case of the filled 2mFo-DFc map
> (test-3_2mFo-DFc_fill.ccp4 - the second-last map generated). This
> comes out as a series of disconnected blobs (it looks rather like a
> mFo-DFc map, but it doesn't match the actual mFo-DFc
> map). When I take the resulting .mtz file and generate the filled map
> in Coot (with or without omission of Rfree flags), on the other
> hand, it seems to come out fine. There are no error messages in the
> log, but I suspect the default method to fill in the missing F_obs
> may be returning /only/ the missing F_obs?
> I've attached a small example image. Red wireframe is the 2mFo-DFc
> unfilled map at 1 sigma; green translucent is the 2mFo-DFc filled map
> at 1 sigma; yellow is the mFo-DFc map at 2 sigma.
> The test structure I'm using is nothing special: 3WSY, picked
> more-or-less at random off the protein data bank. Phenix version is
> 1.9.1692, installed in Fedora 21.
> Have I done something wrong that I'm just not seeing, or is there a
> bug here?
> phenixbb mailing list
> phenixbb at phenix-online.org
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