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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@ebi.ac.uk>
To: "'Pavel Afonine'" <pafonine@lbl.gov>,       "'Armando Albert'"
        <xalbert@iqfr.csic.es>, <phenixbb@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
And
_refine.ls_number_reflns_obs
http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb
er_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@phenix-online.org
<phenixbb-bounces@phenix-online.org> On Behalf Of Pavel Afonine
Sent: 20 October 2020 18:16
To: Armando Albert <xalbert@iqfr.csic.es>; phenixbb@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@bgu.ac.il>
To: phenixbb <phenixbb@phenix-online.org>
Subject: [phenixbb] Fwd: Re:  Number of unique reflections
Message-ID: <787a9a55-8840-44ad-b176-a7d3feae038c@email.android.com>
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 <nwmoriarty@lbl.gov>
To: undisclosed-recipients:;
Subject: [phenixbb] Computational Crystallography Newsletter (CCN)
        submissions
Message-ID:
        <CANkP=2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ@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@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@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>,
        "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
Cc: Christopher Schlicksup <cjschlicksup@lbl.gov>
Subject: [phenixbb] Phenix User Workshop, 17th and 18th of November
Message-ID:
        <CA+umy2aQ8qAhwU-FdDSfeXZ=F-2t_sR0Gq9ZCOcwW-TdaDqJvw@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@lbl.gov <LBenvenue@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@gmail.com>
To: phenixbb@phenix-online.org
Subject: [phenixbb] Anomalous signal
Message-ID:
        <CAPJ-2XxgXgm5jxbq=CBT46STdiPsmbWMKK0WftbMW9_=Q4iROQ@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@colgate.edu>
To: Shramana Chatterjee <schatter90@gmail.com>
Cc: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Anomalous signal
Message-ID:
        <CA+Ey6U5oDeO+s_SkPxj=EJVzvNRMqT5qKEjk+7EtzTvT3FPPrA@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@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@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave@phenix-online.org
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Message: 7
Date: Thu, 5 Nov 2020 10:32:31 +0100
From: Gerg? G?gl <gogl.gergo@gmail.com>
Cc: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] Anomalous signal
Message-ID:
        <CAArrK3Ry-iL+FpqKooNvFfriyTOS6PEDesnN3+xC3PUaPm83uw@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@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@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@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>> Unsubscribe: phenixbb-leave@phenix-online.org
>
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave@phenix-online.org
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Message: 8
Date: Thu, 5 Nov 2020 13:36:16 +0100
From: Almudena Ponce Salvatierra <maps.farma@gmail.com>
To: phenixbb@phenix-online.org
Subject: [phenixbb] mrc maps as a molecular replacement model
Message-ID:
        <CAOggArntNyM2BrTAKD1_hC62vB37OvzbvZhe+2SABNp-8uFrkg@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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