[phenixbb] Fw: Strange behaviour of phenix.maps fill_missing_f_obs

Tristan Croll tristan.croll at qut.edu.au
Thu Feb 5 18:09:24 PST 2015

Hi Pavel,

That does look promising! I'll switch my code over to use that approach instead, and have a play with it. However, I do believe there is a bug in the "kick map" option that may be causing problems for some.

Best regards,


From: Pavel Afonine <pafonine at lbl.gov>
Sent: Friday, 6 February 2015 11:34 AM
To: Tristan Croll; phenixbb at phenix-online.org
Subject: Re: [phenixbb] Fw: Strange behaviour of phenix.maps fill_missing_f_obs

Hi Tristan,

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<mailto: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<mailto:phenixbb at phenix-online.org>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20150206/0b20b6c7/attachment.htm>

More information about the phenixbb mailing list