February 2017 - phenixbb - phenix-online.org

changing mtz from P 31 2 1 to P 32 2 1
by Sebastiano Pasqualato 16 Feb '17

16 Feb '17

Hi guys, is there an utility in phenix to change hand of an mtz file? I’m interested in getting a P 32 2 1 mtz from a P 31 2 1. phenix.refine does handle the refinement in P 32 2 1 even with the P 31 2 1 mtz, but the polder map calculating tools complains about discrepancy between the pdb and the mtz. Thanks in advance, ciao, S -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEOXtalUnit <http://is.gd/IEOXtalUnit>

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Travel to ACA Meeting New Orleans May 26-30 2017
by Terwilliger, Thomas Charles 10 Feb '17

10 Feb '17

Colleagues, Like many of you, we are concerned over the recent upheaval surrounding travel to and from the United States.The ACA is committed to hosting an annual meeting that brings together a diverse community of scientists, no matter what their country of origin. Our mission includes diversity and a desire to foster a global community of structural scientists, in accordance with the principles of the International Union of Crystallography. While we understand any reluctance to travel to the US at this time, we would like to encourage anyone who is interested in attending the meeting in New Orleans this May to register now and to submit an abstract should you wish to present your work. We will offer a full refund of registration costs to anyone who is denied entry into the US or cannot risk the travel because of travel restrictions. We want you to know that all scientists are welcome at the ACA. Sincerely, The Members of the ACA Council Amy Sarjeant, President Tom Terwilliger, Past President Lisa Keefe, Vice President Sue Byram, Treasurer Diana Tomchick, Secretary Tomislav Friscic, Canadian Representative Hanna Dabkowska, IUCr Representative Bill Duax, CEO Marcia Colquhoun, Director of Admin. Services Kristina Vitale, Membership Secretary Please visit our website to learn more about the 2017 ACA Meeting http://www.amercrystalassn.org/2017-meeting-homepage

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Job vacancy University of Manchester (3 positions)
by Colin Levy 10 Feb '17

10 Feb '17

Dear All, Please see below for details of several positions currently being advertised here at the University of Manchester. Many thanks, Colin Research Associate, Structural Biology / Enzymology (3 posts) Closing Date : 13/03/2017 Employment Type : Fixed Term Duration : 2 x 35 months plus 1 x 15 months Faculty / Organisational Unit : Science & Engineering School/Directorate : School of Chemistry Division : Chemical Biology & Biological Chemistry Hours Per week : Full-time Salary : £31,076 to £38,183 per annum Location : Manchester Institute of Biotechnology (MIB) Job Reference : S&E-09634 You will be working on Biotechnology and Biological Sciences Research Council (BBSRC)-funded projects in the group of Professor David Leys at the Manchester Institute of Biotechnology (MIB). These projects focus on structure-function relationship studies and biotechnological application of novel enzymes, and require individuals with a suitable background in structural biology and/or enzymology. You will join a large team of researchers in the Molecular Enzymology group at the MIB, and will receive training in a range of techniques as applied to establishing the structural and functional properties of the target enzymes. All posts are available with immediate effect, posts one and two ending 31 March 2020 and post three ending 31 May 2018. The School of Chemistry is strongly committed to promoting equality and diversity, including the Athena SWAN Charter for gender equality in higher education. The School holds a Silver Award which recognises their good practice in relation to gender; including flexible working arrangements, family-friendly policies, and support to allow staff to achieve a good work-life balance. We particularly welcome applications from women for this post. Appointments will always be made on merit. For further information, please visit http://www.chemistry.manchester.ac.uk/about-us/athena-swan/ Please note that we are unable to respond to enquiries, accept CVs or applications from recruitment agencies. Enquiries about the vacancy, shortlisting and interviews: Professor David Leys Email: david.leys(a)manchester.ac.uk<mailto:[email protected]> General enquiries: Email: hrservices(a)manchester.ac.uk<mailto:[email protected]> Telephone: 0161 275 4499 Technical support: Email: universityofmanchester(a)helpmeapply.co.uk<mailto:[email protected]> Telephone: 01565 818 234 Date of external posting: Thursday, 9 February 2017 This vacancy will close for applications at midnight on the closing date. [cid:[email protected]] Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 c.levy(a)manchester.ac.uk<mailto:[email protected]> Manchester Institute of Biotechnology | University of Manchester | 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN

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solvent masks
by Kajander, Tommi A 10 Feb '17

10 Feb '17

Hi All, Was there a convenient way to make a solvent mask for a region with a model - its been a while - and use that to generate maps (i have a domain that is only partially visible, could not be found be molecular replacement), its there though. Could be that its not well ordered, but I was wondering if the bulk solvent masking is just wiping it out. (basicly something like half a domain, e.g. half of individual beta-strands, are missing.) resolution is bit limited (at best 3 Å) so automated building and refinement doesnt work terribly well. I could just place a model there and make a mask somewhere and include in map calculation? Thanks for suggestions, tommi

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phenix.composite_omit_map
by Dyda 09 Feb '17

09 Feb '17

Dear Phenix BB, I have a moderate resolution structure that I refined using secondary structure restraints (both for nucleic acid and for protein) I'd like to use phenix.composite_omit_map to calculate such a map. Is it possible (and if so how) to make phenix.composite_omit_map to use the same restraints during annealing of the not omitted parts? Thanks! Fred [32m******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:[email protected] Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476710(a)mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *******************************************************************************[m

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Re: [phenixbb] Running Phenix Gui on Debian 8
by Chow, Martin 08 Feb '17

08 Feb '17

I am having troubling running Phenix 1.11.1.2575 gui under Debian 8 (Jessie), and have same results with different computers that are running the same system. I have no problem with previous versions like 1.9 and 1.10. However, with 1.11, Phenix guy won’t run. It complains about Gtk+ or Glib etc and quits. I know these are related to gui tool kits. I have tried Centro5, Centro6, and even compiled it, they all give similar or same complaints. I believe command-line works, but never try. However, simple commands like —version or —-help etc work. I just tried it on Red Hat, 1.11 works without issues. Clearly, it is a problem with the Linux Distro. Thank you. Martin Chow, Ph.D. Biochemistry University of Kentucky ________________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of phenixbb-request(a)phenix-online.org [phenixbb-request(a)phenix-online.org] Sent: Tuesday, February 07, 2017 3:20 PM To: phenixbb(a)phenix-online.org Subject: phenixbb Digest, Vol 135, Issue 4 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Computational Crystallography Newsletter, Volume 8, Number 1 (Nigel Moriarty) 2. Re: Phenix installation on manjaro (Murpholino Peligro) 3. Re: Phenix installation on manjaro (Billy Poon) 4. Re: Phenix installation on manjaro (Murpholino Peligro) 5. Re: Phenix installation on manjaro (Murpholino Peligro) 6. pdbtools atom_selection behavior (wtempel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Feb 2017 13:21:05 -0800 From: Nigel Moriarty <nwmoriarty(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org>, ccp4bb <CCP4BB(a)jiscmail.ac.uk>, developers(a)phenix-online.org, industry(a)phenix-online.org Subject: [phenixbb] Computational Crystallography Newsletter, Volume 8, Number 1 Message-ID: <CANkP=2eK6S4MWS=UJ=wZLXfC5qR9vQpgZEyi91gVv47EvdWQjA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 ? O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> 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(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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pdbtools atom_selection behavior
by wtempel 07 Feb '17

07 Feb '17

Hello all, suppose I would like to remove one alternate conformation B from residue 1 in chain A and set the occupancy of remaining atoms in that residue to 1. phenix.pdbtools alts_minim.pdb occupancies.set=1 \ occupancies.atom_selection=”chain A and resid 1” \ keep=”not (chain A and altid B and resid 1)” \ output.file_name=alts.out.pdb There are better methods to achieve that, but I eventually would like to expand this command to do other “things” to my coordinates. Well, so far I have failed to have the atom_selection to work the way *I* expect. stdout reveals that the program fails to apply a common scope to the command switches, and proceeds to reset occupancies of all atoms. Can this be done on the command line? A minimal (not) working example is attached, and your feedback appreciated. Best regards. Wolfram Tempel

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Phenix installation on manjaro
by Murpholino Peligro 07 Feb '17

07 Feb '17

Dear all. has anyone been lucky with the installation of phenix in manjaro or any other archlinux-based distribution? Thanks Ps. Error looks like http://pastebin.com/WzwrbK8W

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Computational Crystallography Newsletter, Volume 8, Number 1
by Nigel Moriarty 06 Feb '17

06 Feb '17

I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. January 2017 <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf> Articles - Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing Environments <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=10> Short Communications - multi_core_run(), yet another simple tool for embarrassingly parallel jobs <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=6> - Phenix tool to compute a difference map for cryo-EM <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=8> Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens <http://www.phenix-online.org/newsletter/CCN_2017_01.pdf#page=2> 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(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Scale and merge multiple data sets
by Sam Tang 05 Feb '17

05 Feb '17

Dear colleagues Hello again. I would like to scale and merge two different native datasets for a same protein complex (which semed to die off gradually in the beam) using the scale_and_merge tool. The error message was received "Multiple intensity arrays - please specify one: data_labels=I,SIGI data_labels=IPR,SIGPR" However I looked into the log file and I have actually included "data_labels = "IPR,SIGIPR,merged" . Perhaps I have missed something else in the setting? Regards Sam Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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