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

Claudia Millán Nebot cm844 at cam.ac.uk
Tue Nov 10 09:46:19 PST 2020


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, <phenixbb-request at phenix-online.org>
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)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Oct 2020 18:30:16 +0100
> From: "John Berrisford" <jmb at ebi.ac.uk>
> To: "'Pavel Afonine'" <pafonine at lbl.gov>,       "'Armando Albert'"
>         <xalbert at iqfr.csic.es>, <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Number of unique reflections
> Message-ID: <009401d6a706$ad6c8120$08458360$@ebi.ac.uk>
> 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_obs.html>
> 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_number_reflns_obs.html>
>
> 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: phenixbb-bounces at phenix-online.org
> <phenixbb-bounces at phenix-online.org> On Behalf Of Pavel Afonine
> Sent: 20 October 2020 18:16
> To: Armando Albert <xalbert at iqfr.csic.es>; phenixbb at phenix-online.org
> 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 <bshaanan at bgu.ac.il>
> To: phenixbb <phenixbb at phenix-online.org>
> Subject: [phenixbb] Fwd: Re:  Number of unique reflections
> Message-ID: <787a9a55-8840-44ad-b176-a7d3feae038c at email.android.com>
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> ------------------------------
>
> Message: 3
> Date: Mon, 2 Nov 2020 14:38:52 -0800
> From: Nigel Moriarty <nwmoriarty at lbl.gov>
> To: undisclosed-recipients:;
> Subject: [phenixbb] Computational Crystallography Newsletter (CCN)
>         submissions
> Message-ID:
>         <CANkP=
> 2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ at mail.gmail.com>
> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
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> ------------------------------
>
> Message: 4
> Date: Tue, 3 Nov 2020 15:35:00 -0800
> From: Paul Adams <pdadams at lbl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>,
>         "CCP4BB at JISCMAIL.AC.UK" <CCP4BB at jiscmail.ac.uk>
> Cc: Christopher Schlicksup <cjschlicksup at lbl.gov>
> Subject: [phenixbb] Phenix User Workshop, 17th and 18th of November
> Message-ID:
>         <CA+umy2aQ8qAhwU-FdDSfeXZ=
> F-2t_sR0Gq9ZCOcwW-TdaDqJvw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Colleagues,
>
> The Phenix developers will be holding an online *Phenix User Workshop on
> the 17th and 18th of November at 8am-12pm PDT.* These times will work best
> for researchers in North and South America, Europe and Africa. We plan to
> hold a future workshop at a time better suited to researchers in Asia and
> Australasia.
>
> The format of the workshop will be demos of the use of Phenix programs
> combined with slides to explain the theory. We expect an interactive
> meeting where attendees can ask questions for the Phenix team to answer.
>
> The workshop will cover aspects of macromolecular crystallography in
> Phenix, with the final emphasis based on the applicants? research
> interests. To apply please fill out this form
> <https://forms.gle/Q8P6ZC9fYqTkS7qD7>. We will make every effort to
> accommodate all applicants, but may need to defer some requests to a
> future workshop if demand is high. We are hoping this workshop will be a
> success, in which case we plan to host more in the future.
>
> Cheers,
> The Phenix Developer Team
> --
> Paul Adams
> Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (
> http://biosciences.lbl.gov/divisions/mbib)
> Principal Investigator, Computational Crystallography Initiative, LBL (
> http://cci.lbl.gov)
> Vice President for Technology, the Joint BioEnergy Institute (
> http://www.jbei.org)
> Principal Investigator, ALS-ENABLE, Advanced Light Source (
> http://als-enable.lbl.gov)
> Division Deputy for Biosciences, Advanced Light Source (
> https://als.lbl.gov)
> Laboratory Research Manager, ENIGMA Science Focus Area (
> http://enigma.lbl.gov)
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley (
> http://bioeng.berkeley.edu)
> Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (
> http://compbiochem.berkeley.edu)
>
> Building 33, Room 347
> Building 978, Room 4126
> Building 977, Room 180C
> Tel: 1-510-486-4225
> http://cci.lbl.gov/paul
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Ashley Dawn [ AshleyDawn at lbl.gov <LBenvenue at lbl.gov>
> ]
> [ 1-510-486-5455 ]
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> ------------------------------
>
> Message: 5
> Date: Wed, 4 Nov 2020 16:58:47 -0500
> From: Shramana Chatterjee <schatter90 at gmail.com>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Anomalous signal
> Message-ID:
>         <CAPJ-2XxgXgm5jxbq=CBT46STdiPsmbWMKK0WftbMW9_=
> Q4iROQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> How can I find anomalous signal for Zn-metal to be sure whether Zn is
> binding or not, for an already processed dataset?
>
> It would be very helpful if I get any suggestion.
>
> Thank you in advance.
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> ------------------------------
>
> Message: 6
> Date: Wed, 4 Nov 2020 19:05:35 -0500
> From: Roger Rowlett <rrowlett at colgate.edu>
> To: Shramana Chatterjee <schatter90 at gmail.com>
> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Anomalous signal
> Message-ID:
>         <CA+Ey6U5oDeO+s_SkPxj=
> EJVzvNRMqT5qKEjk+7EtzTvT3FPPrA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> You may not need to see an anomalous signal to determine if zinc is bound
> unless you are trying to discriminate from other metals. Zinc will have
> characteristic coordination geometry (tetrahedral typically) and
> characteristic Zn-N and Zn-O bond lengths close to 2.0 A.
>
> Roger Rowlett
>
> On Wed, Nov 4, 2020, 4:59 PM Shramana Chatterjee <schatter90 at gmail.com>
> wrote:
>
> > Hi,
> >
> > How can I find anomalous signal for Zn-metal to be sure whether Zn is
> > binding or not, for an already processed dataset?
> >
> > It would be very helpful if I get any suggestion.
> >
> > Thank you in advance.
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: phenixbb-leave at phenix-online.org
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> ------------------------------
>
> Message: 7
> Date: Thu, 5 Nov 2020 10:32:31 +0100
> From: Gerg? G?gl <gogl.gergo at gmail.com>
> Cc: PHENIX user mailing list <phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Anomalous signal
> Message-ID:
>         <
> CAArrK3Ry-iL+FpqKooNvFfriyTOS6PEDesnN3+xC3PUaPm83uw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> You can try with ANODE to get an anomalous map for your structure.
>
> Gergo
>
> Roger Rowlett <rrowlett at colgate.edu> ezt ?rta (id?pont: 2020. nov. 5., Cs,
> 1:06):
>
> > You may not need to see an anomalous signal to determine if zinc is bound
> > unless you are trying to discriminate from other metals. Zinc will have
> > characteristic coordination geometry (tetrahedral typically) and
> > characteristic Zn-N and Zn-O bond lengths close to 2.0 A.
> >
> > Roger Rowlett
> >
> > On Wed, Nov 4, 2020, 4:59 PM Shramana Chatterjee <schatter90 at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> How can I find anomalous signal for Zn-metal to be sure whether Zn is
> >> binding or not, for an already processed dataset?
> >>
> >> It would be very helpful if I get any suggestion.
> >>
> >> Thank you in advance.
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb
> >> Unsubscribe: phenixbb-leave at phenix-online.org
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
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> ------------------------------
>
> Message: 8
> Date: Thu, 5 Nov 2020 13:36:16 +0100
> From: Almudena Ponce Salvatierra <maps.farma at gmail.com>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] mrc maps as a molecular replacement model
> Message-ID:
>         <
> CAOggArntNyM2BrTAKD1_hC62vB37OvzbvZhe+2SABNp-8uFrkg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi everybody,
>
> I would like to use a cryo-EM map for MR, however, I get an error message
> as I try to provide it to phaser:
>
> "Phenix did not recognize the file type for xxx.mrc"
>
> My Phenix version is 1.17.1-3660-000
>
> What should I do?
>
> Thank you very much
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> End of phenixbb Digest, Vol 180, Issue 1
> ****************************************
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