[phenixbb] phenixbb Digest, Vol 180, Issue 1 : Using a CryoEM density for MR

Dear Almudena, I'm assuming that you were testing the full mr phaser section in phenix and tried the add map ensemble. This expects an mtz containing structure factors, and where certain preparation has been done. A full description of the steps required can be found in a prior publication ( https://www.nature.com/articles/nprot.2015.069?proof=t) from our group. In short, you'll need to first convert your mrc map to structure factors (there a command line utility for this in phenix, called map_to_structure_factors). But you can't input this directly as an ensemble, a series of other steps involving placing the map in a large P1 cell using phenix.cut_out_density (wit the option for_phaser set to True) will also be required for it to work, and you'll need to give information about the center and the extent of your map, as well as an estimation of the errors in the map (in form of an rmsd). Only then you'll be able to use the density for MR. Within the framework of the new version of phaser under development, phasertng, we are working on facilitating this MR approach, making it automatic and robust, and investigating about the best ways to treat the maps and to parameterise their search. This is work in progress but we have already some modes for map preparation for MR within phasertng, so we will also be happy, if you share with us the file off-line, to provide you with the prepared structure factors file. Otherwise, if you need any help in following the steps of the previous protocol, we will also provide the support. Best wishes, Claudia El jue., 5 nov. 2020 a las 12:41, escribió:

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Today's Topics:

1. Re: Number of unique reflections (John Berrisford) 2. Fwd: Re: Number of unique reflections (Boaz Shaanan) 3. Computational Crystallography Newsletter (CCN) submissions (Nigel Moriarty) 4. Phenix User Workshop, 17th and 18th of November (Paul Adams) 5. Anomalous signal (Shramana Chatterjee) 6. Re: Anomalous signal (Roger Rowlett) 7. Re: Anomalous signal (Gerg? G?gl) 8. mrc maps as a molecular replacement model (Almudena Ponce Salvatierra)

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Message: 1 Date: Tue, 20 Oct 2020 18:30:16 +0100 From: "John Berrisford" To: "'Pavel Afonine'" , "'Armando Albert'" , Subject: Re: [phenixbb] Number of unique reflections Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii"

Dear Armando and Pavel

During the deposition process we compare two values

_reflns.number_obs

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_ obs.html http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_... And _refine.ls_number_reflns_obs

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb er_reflns_obs.html http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb...

We expect the number of observed reflections to be higher (or the same) as the number of reflections used in refinement. We would expect that these two mmCIF items handle Friedel pairs consistently - if the number of reflections observed is reported with Friedel pairs separately then the number of reflections in refinement should also report Friedel pairs separately.

My assumption here is that there is a mismatch in reporting these values.

Hope this helps

John

-----Original Message----- From: [email protected] On Behalf Of Pavel Afonine Sent: 20 October 2020 18:16 To: Armando Albert ; [email protected] Subject: Re: [phenixbb] Number of unique reflections

Hi Armando,

...

We have realise that the output mtz and mmcif files duplicate the number of miller indices (the number of unique reflections) with respect to those in the mtz input file. We guessed that this correspond to the friedel pairs,

data handling machinery in Phenix (cctbx) counts F+ and F- as separately, that is (1, 1, 2) and (-1, -1, -2) are two entries, not one.

...

but it is annoying for pdb submission, as the server warns that the observations measured are less that those used in the refinement. What shall we do fro correct this issue?

Perhaps talk to PDB stuff and suggest to make the process less annoying...

I'm not sure what we can do at our end. I guess if we count them as one then I'm sure some one will come around asking 'why you are counting two reflections as one?'.

Pavel

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Message: 2 Date: Tue, 20 Oct 2020 18:16:16 +0000 From: Boaz Shaanan To: phenixbb Subject: [phenixbb] Fwd: Re: Number of unique reflections Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii"

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Message: 3 Date: Mon, 2 Nov 2020 14:38:52 -0800 From: Nigel Moriarty To: undisclosed-recipients:; Subject: [phenixbb] Computational Crystallography Newsletter (CCN) submissions Message-ID: Content-Type: text/plain; charset="utf-8"

Folks

The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 15 DEC 2020. Please consider writing an article of general interest to the community.

The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov