- phenixbb - phenix-online.org

Re: [phenixbb] Questions about refine glycans using PHENIX
by Pavel Afonine 08 Aug '18

08 Aug '18

Hi, yes, as long as the map shows the glycans clearly enough so that you can model them, then there is no problem refining your model using phenix.real_space_refine. Normally, there is no need to add anything special. Now I'm puzzled.. do you have a reason to believe that something isn't working correctly? By the way, we will be at Tsinghua University first week of September running Phenix workshop. We can discuss things while there! All the best, Pavel On 8/7/18 08:16, Miao Gui wrote: > Dear phenix developers, > > I'm a PHENIX user. PHENIX helped me a lot when refining structural > models against cryo-EM maps. > > Recently, I built a structural model of a glycoprotein and added the > glycans using COOT against a 3.4 A cryo-EM map. Then I want to refine > the model using PHENIX.real_space_refine. I always add the second > structure restrains when refining the models against cryo-EM maps. Do > I need to add other restrains for the glycans? Is it appropriate to > refine the glycoprotein using the real_space_refine? > Thank you. > > Best wishes, > > Dr. Miao Gui > Tsinghua University, Beijing > >

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Post Doctoral Research Fellow opportunity - Structural Chemistry Group at MD Anderson Cancer Center's Therapeutics Division.
by Leonard,Paul G 04 Aug '18

04 Aug '18

At MD Anderson, we have been working to eliminate cancer for more than seven decades and are ranked as one of the top two hospitals in cancer care every year since 1990. One of our greatest strengths is our ability to translate today's most promising laboratory findings into tomorrow's new, more effective and less traumatic treatments. We are recruiting exceptional national and international post-doctoral fellowsto join our Structural Chemistry group, part of the Institute for Applied Cancer Science. Applicants must be extremely motivated and possess a strong background in structural biology, including protein expression and purification, crystallization, and X-ray crystallography. Experience using other biophysical techniques would be an advantage. We are seeking only the most dedicated individuals who will join us in our quest to discover, develop, and deliver more effective treatments to our patients. This is a unique opportunity to participate in project-driven drug discovery research within a highly respected academic and clinical setting. We’re tackling cancer and neurodegeneration with a new plan — our Moon Shots Program - one that aims to improve prevention, early detection and treatment. Our research engines fuel innovation along the way. And innovation, collaboration and scale get us there faster. They give us the framework we need for success, and speed up development for new and more effective care. Our Missionis to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative targeted therapeutics, both small molecules and biologics for unmet medical needs. Our work is conducted in an environment that brings together excellence in both academic and pharmaceutical discovery, as evidenced by recent publications. Visit our platforms at https://www.mdanderson.org/cancermoonshots.html Interested individuals should send a cover letter describing their research experience, and a curriculum vitae, to: MD Anderson Therapeutics Division (therapeutics(a)mdanderson.org<mailto:[email protected]>) The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Fw: AsCA 2018 Programme Announcement
by Christopher Squire 03 Aug '18

03 Aug '18

?[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/d231daa0bdac4db99817bc87d65a4b98] Dear Colleagues, The full agenda for the AsCA 2018/CRYSTAL 32 Conference<http://asca2018.org/programme/> is now available online. We invite you to explore our programme of oral presentations, poster presentations, and workshops, displaying outstanding science from Asia, Australia and New Zealand, and from around the world. If you haven't already, register today<http://asca2018.org/registration/> at the early-bird rate to connect with the scientific community, and our speakers<http://asca2018.org/speakers/>, and start planning your schedule. It's peak season in December so we recommend you book your accommodation<http://asca2018.org/accommodation/> early. Likewise, if you haven't submitted your abstract yet, we kindly request your support by submitting contributions to the AsCA 2018/CRYSTAL 32 conference at your earliest convenience before the deadlines (1 September 2018 for Oral, 1 November 2018 for Poster). The online abstract submission link is http://asca2018.org/call-for-abstracts/. The conference will run from 2-5 December 2018. We look forward to seeing you there. In the meantime, if you have any questions please visit the conference website<http://asca2018.org/> or contact us via email<mailto:[email protected]?subject=AsCA%20inquiry>. Kind regards, Dr. Christopher Squire (University of Auckland), Professor Ted Baker (University of Auckland), Professor Kurt Krause (University of Otago) and the AsCA 2018/CRYSTAL 32 Committee. [https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-pub…] ________________________________ ?

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Workshop on nMX at ECM31, the programme now online
by John R Helliwell 02 Aug '18

02 Aug '18

Dear Colleagues, The Workshop on nMX at ECM31, the programme is now online at:- https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php There is still time to register. Best wishes, John Emeritus Professor John R Helliwell DSc

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Error building Amber interface to phenix
by Roger Shek 31 Jul '18

31 Jul '18

I am trying to build the amber interface to phenix, but encounter an error. Running OpenSUSE15. Anyone have any ideas? phenix.build_amber_interface Phenix modules found : /opt/phenix-1.13-2998/modules/phenix $AMBERHOME set : /home/roger/bin/Amber/amber18 Linking AMBERHOME to Phenix modules Not linking $AMBERHOME into Phenix modules directory because there is already a link and it points to the same directory as $AMBERHOME. $AMBERHOME : /home/roger/bin/Amber/amber18 Phenix link: /opt/phenix-1.13-2998/modules/amber Building amber_adaptbx ~> libtbx.configure amber Python: 2.7.14 "/opt/phenix-1.13-2998/base/bin/python2.7" Compiler: default Build mode: release Warning level: 0 Precompiled Headers: False Static libraries: False Static exe: False Scan Boost headers: False Write full flex_fwd.h files: False Build Boost.Python extensions: True Define BOOST_PYTHON_NO_PY_SIGNATURES: False Define BOOST_PYTHON_BOOL_INT_STRICT: True Enable OpenMP if possible: False Boost threads enabled: False Enable CUDA: False Use opt_resources if available: False Use environment flags: False Enable C++11: False Python3 migration warning policy: None command_version_suffix: 1.13-2998 Relocatable paths anchored at: /opt/phenix-1.13-2998/build Top-down list of all modules involved: prime "/opt/phenix-1.13-2998/modules/cctbx_project/prime" iota "/opt/phenix-1.13-2998/modules/cctbx_project/iota" xia2 "/opt/phenix-1.13-2998/modules/xia2" xfel "/opt/phenix-1.13-2998/modules/cctbx_project/xfel" dials "/opt/phenix-1.13-2998/modules/dials" simtbx "/opt/phenix-1.13-2998/modules/cctbx_project/simtbx" cma_es "/opt/phenix-1.13-2998/modules/cctbx_project/cma_es" labelit "/opt/phenix-1.13-2998/modules/labelit" rstbx "/opt/phenix-1.13-2998/modules/cctbx_project/rstbx" spotfinder "/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder" annlib+adaptbx "/opt/phenix-1.13-2998/modules/annlib" "/opt/phenix-1.13-2998/modules/annlib_adaptbx" phenix "/opt/phenix-1.13-2998/modules/phenix" reel "/opt/phenix-1.13-2998/modules/reel" wxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx" phaser_regression "/opt/phenix-1.13-2998/modules/phaser_regression" phaser "/opt/phenix-1.13-2998/modules/phaser" tntbx "/opt/phenix-1.13-2998/modules/tntbx" solve_resolve "/opt/phenix-1.13-2998/modules/solve_resolve" muscle "/opt/phenix-1.13-2998/modules/muscle" ksdssp "/opt/phenix-1.13-2998/modules/ksdssp" pulchra "/opt/phenix-1.13-2998/modules/pulchra" phenix_html "/opt/phenix-1.13-2998/modules/phenix_html" phenix_regression "/opt/phenix-1.13-2998/modules/phenix_regression" elbow "/opt/phenix-1.13-2998/modules/elbow" Plex "/opt/phenix-1.13-2998/modules/Plex" PyQuante "/opt/phenix-1.13-2998/modules/PyQuante" crys3d "/opt/phenix-1.13-2998/modules/cctbx_project/crys3d" gltbx "/opt/phenix-1.13-2998/modules/cctbx_project/gltbx" amber+adaptbx "/opt/phenix-1.13-2998/modules/amber" "/opt/phenix-1.13-2998/modules/amber_adaptbx" mmtbx "/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx" suitename "/opt/phenix-1.13-2998/modules/suitename" king "/opt/phenix-1.13-2998/modules/king" probe "/opt/phenix-1.13-2998/modules/probe" reduce "/opt/phenix-1.13-2998/modules/reduce" iotbx "/opt/phenix-1.13-2998/modules/cctbx_project/iotbx" ccp4io+adaptbx "/opt/phenix-1.13-2998/modules/ccp4io" "/opt/phenix-1.13-2998/modules/ccp4io_adaptbx" dxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx" cbflib+adaptbx "/opt/phenix-1.13-2998/modules/cbflib" "/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx" smtbx "/opt/phenix-1.13-2998/modules/cctbx_project/smtbx" ucif "/opt/phenix-1.13-2998/modules/cctbx_project/ucif" cctbx "/opt/phenix-1.13-2998/modules/cctbx_project/cctbx" scitbx "/opt/phenix-1.13-2998/modules/cctbx_project/scitbx" fable "/opt/phenix-1.13-2998/modules/cctbx_project/fable" omptbx "/opt/phenix-1.13-2998/modules/cctbx_project/omptbx" boost+adaptbx "/opt/phenix-1.13-2998/modules/boost" "/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx" tbxx "/opt/phenix-1.13-2998/modules/cctbx_project/tbxx" chiltbx "/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx" libtbx "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx" Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh" Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh" Creating files in build directory: "/opt/phenix-1.13-2998/build" dispatcher_include_template.sh dispatcher_head.sh Traceback (most recent call last): File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2462, in <module> warm_start(sys.argv) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2456, in warm_start env.refresh() File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1615, in refresh self.write_lib_dispatcher_head() File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1248, in write_lib_disp atcher_head target_file=self.under_build(target_file, return_relocatable_path=True)) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1146, in write_bin_sh_d ispatcher target_file.chmod(0755) File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py", line 279, in chmod return os.chmod(abs(self), *args, **kwds) OSError: [Errno 1] Operation not permitted: '/opt/phenix-1.13-2998/build/dispatcher_head.sh' -- Roger Shek Stony Brook University Graduate Student in Biochemistry and Structural Biology (PhD) Stony Brook Integrative Structural Biology Organization <http://sbinststrbio.com/> Cell: (808) 386-3879 Website: https://www.rogershek.com

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Ligand occupancy and conformational change
by Xavier Brazzolotto 25 Jul '18

25 Jul '18

I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet. As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear. How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ? Thank you for your help Xavier

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How to use phaser gyre and gimble in phenix
by Meinke, Gretchen 20 Jul '18

20 Jul '18

Hello again-- I have partially solved my silly problem: This is how to use it. phenix.gyre_and_gimble I may write back for more specifics, if my MR remains unsolved. Thanks! Gretchen

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How to use phaser gyre and gimble in phenix
by Meinke, Gretchen 19 Jul '18

19 Jul '18

Hi! I have a challenging MR problem and maybe phenix.phaser gyre and gimble will help. My molecule is flexible horsehoe shaped slinky, there are multiples in the unit cell (maybe 8-12??). My data is medium resolution 3.5 maybe. There are good homology models (also flexible!) It seems to have 1-2 hinge points (or 2-3 domains). I saw your publication "Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement" Acta Cryst. (2018). D74, 279–289 and that describes exactly what I would like to do. One problem, I cannot at all figure out how to use gyre in gimble in phenix. I cannot find it in the GUI, and am unclear how to run it as a script. It looks super useful and would love to use it. Any help, a script, etc would be most appreciated! Thanks! Gretchen

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FW: Occupancy / alternate conformation Refinement
by Schulz, Eike-Christian 18 Jul '18

18 Jul '18

Dear all, In one of my structures I appear to have a mixed state between a covalently bound intermediate and the free substrate occupying _almost_ the same position. I can model the states nicely in coot, but during refinement the molecules “fly” apart - although the occupancy was limited to 0.5 for their overlapping atoms. I have tried to model the free ligand as an alternate conformation of the covalent intermediate: HETATM 852 N ASB A 110 10.523 15.702 10.022 1.00 14.48 N HETATM 853 CA ASB A 110 9.974 15.713 8.664 1.00 15.11 C HETATM 854 C ASB A 110 8.635 16.385 8.683 1.00 14.31 C HETATM 855 O ASB A 110 8.563 17.443 9.233 1.00 13.03 O HETATM 856 CB ASB A 110 10.053 14.307 8.091 1.00 11.72 C HETATM 857 CG ASB A 110 9.774 14.157 6.621 1.00 15.26 C HETATM 858 OD1 ASB A 110 10.688 14.485 5.644 1.00 19.29 O HETATM 859 OD2 ASB A 110 8.693 13.880 6.340 1.00 13.36 O HETATM 860 C1 AASB A 110 10.637 15.649 3.353 0.50 27.61 C HETATM 861 C2 AASB A 110 10.231 14.480 4.266 0.50 32.98 C HETATM 862 O1 AASB A 110 11.505 16.454 3.690 0.50 31.63 O HETATM 863 O2 AASB A 110 10.085 15.787 2.280 0.50 21.80 O HETATM 4742 O2 BASB A 110 10.072 15.815 2.191 0.50 24.78 O HETATM 4743 C1 BASB A 110 10.573 15.717 3.221 0.50 28.20 C HETATM 4744 O1 BASB A 110 11.449 16.458 3.619 0.50 22.71 O HETATM 4745 C2 BASB A 110 10.107 14.567 4.152 0.50 19.02 C HETATM 4746 F BASB A 110 9.287 13.735 3.610 0.50 34.13 F Although I have provided a new CIF file for the ligand named according to the alternate conformation this causes phenix to crash. How can I correctly refine these overlapping atoms ? Thanks for your advice, Eike

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n_gaussian tables?
by Aaron Oakley 17 Jul '18

17 Jul '18

Hi Phenixers, I gather that the wk1995 and it1992 scattering tables come from Waasmaier & Kirfe (1995), Acta Cryst. A51, 416-431 and the International Tables Vol C 1992 respectively. Can someone please tell me from where the n_gaussian scattering tables are derived? With thanks, a++

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