<div dir="ltr"><div class="gmail_quote"><div dir="ltr"><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font size="2"><span style="font-family:arial,helvetica,sans-serif"><span style="border-collapse:collapse;color:rgb(34,34,34)"><div>Dear Almudena,</div><div><br></div><div>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 (<a href="https://www.nature.com/articles/nprot.2015.069?proof=t" target="_blank">https://www.nature.com/articles/nprot.2015.069?proof=t</a>) 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.</div><div><br></div><div>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.</div><div><br></div><div>Best wishes,</div><div><br></div><div>Claudia</div><div><br></div></span></span></font></div></div></div></div></div></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue., 5 nov. 2020 a las 12:41, <<a href="mailto:phenixbb-request@phenix-online.org" target="_blank">phenixbb-request@phenix-online.org</a>> escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send phenixbb mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Number of unique reflections (John Berrisford)<br>
2. Fwd: Re: Number of unique reflections (Boaz Shaanan)<br>
3. Computational Crystallography Newsletter (CCN) submissions<br>
(Nigel Moriarty)<br>
4. Phenix User Workshop, 17th and 18th of November (Paul Adams)<br>
5. Anomalous signal (Shramana Chatterjee)<br>
6. Re: Anomalous signal (Roger Rowlett)<br>
7. Re: Anomalous signal (Gerg? G?gl)<br>
8. mrc maps as a molecular replacement model<br>
(Almudena Ponce Salvatierra)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 20 Oct 2020 18:30:16 +0100<br>
From: "John Berrisford" <<a href="mailto:jmb@ebi.ac.uk" target="_blank">jmb@ebi.ac.uk</a>><br>
To: "'Pavel Afonine'" <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>>, "'Armando Albert'"<br>
<<a href="mailto:xalbert@iqfr.csic.es" target="_blank">xalbert@iqfr.csic.es</a>>, <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] Number of unique reflections<br>
Message-ID: <009401d6a706$ad6c8120$08458360$@<a href="http://ebi.ac.uk" rel="noreferrer" target="_blank">ebi.ac.uk</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear Armando and Pavel<br>
<br>
During the deposition process we compare two values<br>
<br>
_reflns.number_obs<br>
<a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_obs.html" rel="noreferrer" target="_blank">http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_<br>
obs.html</a><br>
And<br>
_refine.ls_number_reflns_obs<br>
<a href="http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_number_reflns_obs.html" rel="noreferrer" target="_blank">http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb<br>
er_reflns_obs.html</a><br>
<br>
We expect the number of observed reflections to be higher (or the same) as<br>
the number of reflections used in refinement. <br>
We would expect that these two mmCIF items handle Friedel pairs consistently<br>
- if the number of reflections observed is reported with Friedel pairs<br>
separately then the number of reflections in refinement should also report<br>
Friedel pairs separately.<br>
<br>
My assumption here is that there is a mismatch in reporting these values. <br>
<br>
Hope this helps<br>
<br>
John<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a><br>
<<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>> On Behalf Of Pavel Afonine<br>
Sent: 20 October 2020 18:16<br>
To: Armando Albert <<a href="mailto:xalbert@iqfr.csic.es" target="_blank">xalbert@iqfr.csic.es</a>>; <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: Re: [phenixbb] Number of unique reflections<br>
<br>
Hi Armando,<br>
<br>
> We have realise that the output mtz and mmcif files duplicate the <br>
> number of miller indices (the number of unique reflections) with <br>
> respect to those in the mtz input file. We guessed that this <br>
> correspond to the friedel pairs,<br>
<br>
data handling machinery in Phenix (cctbx) counts F+ and F- as separately,<br>
that is (1, 1, 2) and (-1, -1, -2) are two entries, not one.<br>
<br>
> but it is annoying for pdb submission, as the server warns that the<br>
observations measured are less that those used in the refinement.<br>
> What shall we do fro correct this issue?<br>
<br>
Perhaps talk to PDB stuff and suggest to make the process less annoying...<br>
<br>
I'm not sure what we can do at our end. I guess if we count them as one then<br>
I'm sure some one will come around asking 'why you are counting two<br>
reflections as one?'.<br>
<br>
Pavel<br>
<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 20 Oct 2020 18:16:16 +0000<br>
From: Boaz Shaanan <<a href="mailto:bshaanan@bgu.ac.il" target="_blank">bshaanan@bgu.ac.il</a>><br>
To: phenixbb <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
Subject: [phenixbb] Fwd: Re: Number of unique reflections<br>
Message-ID: <<a href="mailto:787a9a55-8840-44ad-b176-a7d3feae038c@email.android.com" target="_blank">787a9a55-8840-44ad-b176-a7d3feae038c@email.android.com</a>><br>
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<br>
Message: 3<br>
Date: Mon, 2 Nov 2020 14:38:52 -0800<br>
From: Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank">nwmoriarty@lbl.gov</a>><br>
To: undisclosed-recipients:;<br>
Subject: [phenixbb] Computational Crystallography Newsletter (CCN)<br>
submissions<br>
Message-ID:<br>
<CANkP=<a href="mailto:2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ@mail.gmail.com" target="_blank">2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Folks<br>
<br>
The deadline for submissions to the Computational Crystallography<br>
Newsletter (CCN) is 15 DEC 2020. Please consider writing an article of<br>
general interest to the community.<br>
<br>
The Computational Crystallography Newsletter (CCN) is an electronic<br>
newsletter for structural biologists, and is published online every 6<br>
months. Feature articles, meeting announcements and reports can be<br>
submitted to me at any time for consideration. Submission of text by<br>
email or word-processing files using the CCN templates is requested.<br>
Past newsletters and a Microsoft Word template are available at<br>
<a href="http://www.phenix-online.org/newsletter" rel="noreferrer" target="_blank">www.phenix-online.org/newsletter</a>.<br>
<br>
Cheers<br>
<br>
Nigel<br>
<br>
---<br>
Nigel W. Moriarty<br>
Building 33R0349, Molecular Biophysics and Integrated Bioimaging<br>
Lawrence Berkeley National Laboratory<br>
Berkeley, CA 94720-8235<br>
Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov" rel="noreferrer" target="_blank">CCI.LBL.gov</a><br>
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Message: 4<br>
Date: Tue, 3 Nov 2020 15:35:00 -0800<br>
From: Paul Adams <<a href="mailto:pdadams@lbl.gov" target="_blank">pdadams@lbl.gov</a>><br>
To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>>,<br>
"<a href="mailto:CCP4BB@JISCMAIL.AC.UK" target="_blank">CCP4BB@JISCMAIL.AC.UK</a>" <<a href="mailto:CCP4BB@jiscmail.ac.uk" target="_blank">CCP4BB@jiscmail.ac.uk</a>><br>
Cc: Christopher Schlicksup <<a href="mailto:cjschlicksup@lbl.gov" target="_blank">cjschlicksup@lbl.gov</a>><br>
Subject: [phenixbb] Phenix User Workshop, 17th and 18th of November<br>
Message-ID:<br>
<CA+umy2aQ8qAhwU-FdDSfeXZ=<a href="mailto:F-2t_sR0Gq9ZCOcwW-TdaDqJvw@mail.gmail.com" target="_blank">F-2t_sR0Gq9ZCOcwW-TdaDqJvw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Colleagues,<br>
<br>
The Phenix developers will be holding an online *Phenix User Workshop on<br>
the 17th and 18th of November at 8am-12pm PDT.* These times will work best<br>
for researchers in North and South America, Europe and Africa. We plan to<br>
hold a future workshop at a time better suited to researchers in Asia and<br>
Australasia.<br>
<br>
The format of the workshop will be demos of the use of Phenix programs<br>
combined with slides to explain the theory. We expect an interactive<br>
meeting where attendees can ask questions for the Phenix team to answer.<br>
<br>
The workshop will cover aspects of macromolecular crystallography in<br>
Phenix, with the final emphasis based on the applicants? research<br>
interests. To apply please fill out this form<br>
<<a href="https://forms.gle/Q8P6ZC9fYqTkS7qD7" rel="noreferrer" target="_blank">https://forms.gle/Q8P6ZC9fYqTkS7qD7</a>>. We will make every effort to<br>
accommodate all applicants, but may need to defer some requests to a<br>
future workshop if demand is high. We are hoping this workshop will be a<br>
success, in which case we plan to host more in the future.<br>
<br>
Cheers,<br>
The Phenix Developer Team<br>
-- <br>
Paul Adams<br>
Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (<br>
<a href="http://biosciences.lbl.gov/divisions/mbib" rel="noreferrer" target="_blank">http://biosciences.lbl.gov/divisions/mbib</a>)<br>
Principal Investigator, Computational Crystallography Initiative, LBL (<br>
<a href="http://cci.lbl.gov" rel="noreferrer" target="_blank">http://cci.lbl.gov</a>)<br>
Vice President for Technology, the Joint BioEnergy Institute (<br>
<a href="http://www.jbei.org" rel="noreferrer" target="_blank">http://www.jbei.org</a>)<br>
Principal Investigator, ALS-ENABLE, Advanced Light Source (<br>
<a href="http://als-enable.lbl.gov" rel="noreferrer" target="_blank">http://als-enable.lbl.gov</a>)<br>
Division Deputy for Biosciences, Advanced Light Source (<a href="https://als.lbl.gov" rel="noreferrer" target="_blank">https://als.lbl.gov</a>)<br>
Laboratory Research Manager, ENIGMA Science Focus Area (<br>
<a href="http://enigma.lbl.gov" rel="noreferrer" target="_blank">http://enigma.lbl.gov</a>)<br>
Adjunct Professor, Department of Bioengineering, U.C. Berkeley (<br>
<a href="http://bioeng.berkeley.edu" rel="noreferrer" target="_blank">http://bioeng.berkeley.edu</a>)<br>
Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (<br>
<a href="http://compbiochem.berkeley.edu" rel="noreferrer" target="_blank">http://compbiochem.berkeley.edu</a>)<br>
<br>
Building 33, Room 347<br>
Building 978, Room 4126<br>
Building 977, Room 180C<br>
Tel: 1-510-486-4225<br>
<a href="http://cci.lbl.gov/paul" rel="noreferrer" target="_blank">http://cci.lbl.gov/paul</a><br>
<br>
Lawrence Berkeley Laboratory<br>
1 Cyclotron Road<br>
BLDG 33R0345<br>
Berkeley, CA 94720, USA.<br>
<br>
Executive Assistant: Ashley Dawn [ <a href="mailto:AshleyDawn@lbl.gov" target="_blank">AshleyDawn@lbl.gov</a> <<a href="mailto:LBenvenue@lbl.gov" target="_blank">LBenvenue@lbl.gov</a>> ]<br>
[ 1-510-486-5455 ]<br>
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<br>
Message: 5<br>
Date: Wed, 4 Nov 2020 16:58:47 -0500<br>
From: Shramana Chatterjee <<a href="mailto:schatter90@gmail.com" target="_blank">schatter90@gmail.com</a>><br>
To: <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: [phenixbb] Anomalous signal<br>
Message-ID:<br>
<CAPJ-2XxgXgm5jxbq=CBT46STdiPsmbWMKK0WftbMW9_=<a href="mailto:Q4iROQ@mail.gmail.com" target="_blank">Q4iROQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
How can I find anomalous signal for Zn-metal to be sure whether Zn is<br>
binding or not, for an already processed dataset?<br>
<br>
It would be very helpful if I get any suggestion.<br>
<br>
Thank you in advance.<br>
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<br>
Message: 6<br>
Date: Wed, 4 Nov 2020 19:05:35 -0500<br>
From: Roger Rowlett <<a href="mailto:rrowlett@colgate.edu" target="_blank">rrowlett@colgate.edu</a>><br>
To: Shramana Chatterjee <<a href="mailto:schatter90@gmail.com" target="_blank">schatter90@gmail.com</a>><br>
Cc: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] Anomalous signal<br>
Message-ID:<br>
<CA+Ey6U5oDeO+s_SkPxj=<a href="mailto:EJVzvNRMqT5qKEjk%2B7EtzTvT3FPPrA@mail.gmail.com" target="_blank">EJVzvNRMqT5qKEjk+7EtzTvT3FPPrA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
You may not need to see an anomalous signal to determine if zinc is bound<br>
unless you are trying to discriminate from other metals. Zinc will have<br>
characteristic coordination geometry (tetrahedral typically) and<br>
characteristic Zn-N and Zn-O bond lengths close to 2.0 A.<br>
<br>
Roger Rowlett<br>
<br>
On Wed, Nov 4, 2020, 4:59 PM Shramana Chatterjee <<a href="mailto:schatter90@gmail.com" target="_blank">schatter90@gmail.com</a>><br>
wrote:<br>
<br>
> Hi,<br>
><br>
> How can I find anomalous signal for Zn-metal to be sure whether Zn is<br>
> binding or not, for an already processed dataset?<br>
><br>
> It would be very helpful if I get any suggestion.<br>
><br>
> Thank you in advance.<br>
> _______________________________________________<br>
> phenixbb mailing list<br>
> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
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<br>
Message: 7<br>
Date: Thu, 5 Nov 2020 10:32:31 +0100<br>
From: Gerg? G?gl <<a href="mailto:gogl.gergo@gmail.com" target="_blank">gogl.gergo@gmail.com</a>><br>
Cc: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] Anomalous signal<br>
Message-ID:<br>
<<a href="mailto:CAArrK3Ry-iL%2BFpqKooNvFfriyTOS6PEDesnN3%2BxC3PUaPm83uw@mail.gmail.com" target="_blank">CAArrK3Ry-iL+FpqKooNvFfriyTOS6PEDesnN3+xC3PUaPm83uw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
You can try with ANODE to get an anomalous map for your structure.<br>
<br>
Gergo<br>
<br>
Roger Rowlett <<a href="mailto:rrowlett@colgate.edu" target="_blank">rrowlett@colgate.edu</a>> ezt ?rta (id?pont: 2020. nov. 5., Cs,<br>
1:06):<br>
<br>
> You may not need to see an anomalous signal to determine if zinc is bound<br>
> unless you are trying to discriminate from other metals. Zinc will have<br>
> characteristic coordination geometry (tetrahedral typically) and<br>
> characteristic Zn-N and Zn-O bond lengths close to 2.0 A.<br>
><br>
> Roger Rowlett<br>
><br>
> On Wed, Nov 4, 2020, 4:59 PM Shramana Chatterjee <<a href="mailto:schatter90@gmail.com" target="_blank">schatter90@gmail.com</a>><br>
> wrote:<br>
><br>
>> Hi,<br>
>><br>
>> How can I find anomalous signal for Zn-metal to be sure whether Zn is<br>
>> binding or not, for an already processed dataset?<br>
>><br>
>> It would be very helpful if I get any suggestion.<br>
>><br>
>> Thank you in advance.<br>
>> _______________________________________________<br>
>> phenixbb mailing list<br>
>> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
>> Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a><br>
><br>
> _______________________________________________<br>
> phenixbb mailing list<br>
> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
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Message: 8<br>
Date: Thu, 5 Nov 2020 13:36:16 +0100<br>
From: Almudena Ponce Salvatierra <<a href="mailto:maps.farma@gmail.com" target="_blank">maps.farma@gmail.com</a>><br>
To: <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
Subject: [phenixbb] mrc maps as a molecular replacement model<br>
Message-ID:<br>
<<a href="mailto:CAOggArntNyM2BrTAKD1_hC62vB37OvzbvZhe%2B2SABNp-8uFrkg@mail.gmail.com" target="_blank">CAOggArntNyM2BrTAKD1_hC62vB37OvzbvZhe+2SABNp-8uFrkg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi everybody,<br>
<br>
I would like to use a cryo-EM map for MR, however, I get an error message<br>
as I try to provide it to phaser:<br>
<br>
"Phenix did not recognize the file type for xxx.mrc"<br>
<br>
My Phenix version is 1.17.1-3660-000<br>
<br>
What should I do?<br>
<br>
Thank you very much<br>
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End of phenixbb Digest, Vol 180, Issue 1<br>
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