- phenixbb - phenix-online.org

Re: [phenixbb] Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Thank you for your valuable Edward, Patrick, Francis. I will try with your suggestions. And let you know the results. On 4 May 2016 20:03, "Edward A. Berry" <BerryE(a)upstate.edu> wrote: On 05/04/2016 10:17 AM, Patrick Loll wrote: > You won’t see peaks in the self-rotation function unless the AU contains > non-crystallographic rotational symmetry, which frequently is not the case > (just because you have multiple copies of your protein in the AU does not > imply that they are arranged in any specific, symmetric manner). And even > if there is rotational NCS, if the axis of rotation is parallel to a > crystal symmetry operator, the effect of the NCS will be masked. So > everything may be working as it should. > > If you’re not certain if you have the program working correctly, then I > suggest that you find a structure in the PDB that contains rotational NCS, > download the structure factors, and calculate the self-rotation map, as a > positive control. > > Try bacterioferritin (in a low-symmetry space group) or GroEL ! > On 4 May 2016, at 12:10 AM, Sharan Karade <sharankarade(a)gmail.com> wrote: >> >> Hello everyone, >> >> i am working on data set which has resolution of 2.8 A >> space group C2, the protein have 394 a a . when i estimate Mathews >> coefficient it shows four to five molecules in asymmetric unit. when i try >> to get self rotation function Map by default parameter (10A-3A and 25 >> radius of integration) i was not getting any peak at all 180, 90, 120, 60. >> Or radius of integration affect the results. >> >> Can anybody please help me to sort out with this problem, welcome for >> suggestions, thanks in advance. >> >> -- >> Sharan >> C/O Dr. J V Pratap >> Senior Research Fellow, >> CSIR-Central Drug Research Institute, >> Lucknow >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > > > > > --------------------------------------------------------------------------------------- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Director, Biochemistry Graduate Program > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.loll(a)drexelmed.edu > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > >

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Self Rotation Function
by Sharan Karade 04 May '16

04 May '16

Hello everyone, i am working on data set which has resolution of 2.8 A space group C2, the protein have 394 a a . when i estimate Mathews coefficient it shows four to five molecules in asymmetric unit. when i try to get self rotation function Map by default parameter (10A-3A and 25 radius of integration) i was not getting any peak at all 180, 90, 120, 60. Or radius of integration affect the results. Can anybody please help me to sort out with this problem, welcome for suggestions, thanks in advance. -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Phenix.multi_crystal_average
by Sam Tang 03 May '16

03 May '16

Hello colleagues May I enquire if the captioned programme is still supported in the latest version of Phenix and, if not, which programme is now in place for this? Thanks in advance. Cheers Sam Tang Biochemistry Programme, School of Life Sciences, CUHK

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CCN submissions
by Nigel Moriarty 02 May '16

02 May '16

Folks Calling for articles and short communications of interest to structural biologists. The initial deadline for submission in the July 2016 issue is 1 June 2016. 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, Physical Biosciences Division 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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Refmac error using PDB coordinates generated by Phenix PDB File Editor
by Xiao Lei 29 Apr '16

29 Apr '16

Hi Phenixbb members, I'm using Phenix PDB File Editor under Phenix GUI "Model Tool" to change occupancy of two short 7 polyalanine alpha helix peptide chain (chain I and K, placed in reverse orientation of each other in one region (or density blob) of my model, each chain half occupancy) , I can change the occupancy very easily with the tool, but I have two types of errors using the coordinates generated by the tool in Refmac. 1. If I set chain ID of chain K to chain I with the same residue number with half occupancy but in reverse order (Chain I, Ala7th--13th 0.5 occupancy and Chain I, Ala7th--13th 0.5 occupancy) , Refmac could not refine the model with an error message below: I am reading library. Please wait. mon_lib.cif ERROR : ALA : duplicated atom_name : "N ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CA ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "CB ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "C ". chain: II residue: 7 ERROR : ALA : duplicated atom_name : "O ". chain: II residue: 7 IERR = 1 There is an error. See above ===> Error: Fatal error. Cannot continue. I understand Refmac can not allow two peptide chain with the same ID and residue number if both peptides are full occupancy (1), but why in this case even half occupancy of the same chain ID and residue number is not tolerated? 2. If I set chain ID of chain K and chain I half occupancy (Chain K, Ala7th--13th 0.5 occupancy and chain I, Ala7th--13th 0.5 occupancy) , put chain K and chain I in the same density blob with reverse direction, and run Refmac, this time Refmac can finish but gave me error message in log file as below: I am reading library. Please wait. mon_lib.cif INFO: link is found (not be used) dist= 1.486 ideal_dist= 1.240 ch:II res: 7 ALA at:N .->ch:KK res: 11 ALA at:O . INFO: link is found (not be used) dist= 1.625 ideal_dist= 1.080 ch:II res: 8 ALA at:O .->ch:KK res: 9 ALA at:O . INFO: link is found (not be used) dist= 1.584 ideal_dist= 1.400 ch:II res: 10 ALA at:N .->ch:KK res: 11 ALA at:N . INFO: link is found (not be used) dist= 1.397 ideal_dist= 1.530 ch:II res: 10 ALA at:CB .->ch:KK res: 11 ALA at:CB . INFO: link is found (not be used) dist= 1.153 ideal_dist= 1.400 ch:II res: 11 ALA at:N .->ch:KK res: 10 ALA at:N . INFO: link is found (not be used) dist= 1.820 ideal_dist= 1.524 ch:II res: 11 ALA at:CA .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 0.888 ideal_dist= 1.530 ch:II res: 11 ALA at:CB .->ch:KK res: 10 ALA at:CB . INFO: link is found (not be used) dist= 1.808 ideal_dist= 1.530 ch:II res: 12 ALA at:CB .->ch:KK res: 9 ALA at:CB . INFO: link is found (not be used) dist= 1.764 ideal_dist= 1.400 ch:II res: 13 ALA at:N .->ch:KK res: 7 ALA at:N . -------------------------------- I do not know why Refmac gave me this message, is it because the two helix chain (I and K) are placed in the same region, even though both with 0.5 occupancy of both chain, Refmac still automatically tries to connect the main chain atom between two different chains (I and K) because main chain atoms are placed too close to each other (Refmac think there is a link between them?) ? 3. In summary, should I use Phenix Refine instead of Refmac to handle the pdb coordinates generated by Phenix PDB file editor because Phenix Refine may have better compatibility? Thanks in advance.

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build two helix run in opposite direction and set half occupancy or each in Coot
by Xiao Lei 29 Apr '16

29 Apr '16

Hi Phenixbb members, Is there a way in the Coot GUI that I can build two helix of the same sequence (or just short 5aa or 6aa peptide chains of the same sequence) that run in the opposite direction (180 degree opposite direction) of each other and set half occupancy of each peptide chain? I tried to use Calculate---> Model/fit/refine/----> add alternative conformation, but it seems I only have two options: "split single residue at C-alpha" or "split all of a single residue", which are applying to single residue only, not a short peptide chain. Thanks.

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Re: [phenixbb] Rosetta refine compilation issue Centos 7
by ludovic Pecqueur 29 Apr '16

29 Apr '16

Dear Phenix developers, This is a feedback from a previous post started a long time ago when I was trying to install the rosetta interface for phenix in Centos 7. As a reminder, I could compile Rosetta with './scons.py -j8' without problem but rosetta.build_phenix_interface exited with an error message related to python. I had given up for some time but I tried again today with more luck. setting up PYTHONHOME as previously suggested was breaking something: which python /usr/bin/python python -c "import site" returns no error > export PYTHONHOME=/usr/bin/python (so the distribution's python) python -c "import site" returns "no module named site" unset PYTHONHOME python -c "import site" returns no error message. adding the path to my local PYTHON with export PATH=/where my local Python 2.7 is/bin/:$PATH was the correct fix and I could finally run rosetta.build_phenix_interface without errors. Cheers Ludovic. On Sep 28, 2015, at 3:24 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 8 > Date: Thu, 24 Sep 2015 16:43:40 +0200 > From: ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> > To: Paul Adams <pdadams(a)lbl.gov> > Cc: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Rosetta refine compilation issue Centos 7 > Message-ID: > <0CB7F2F9-4E89-4598-92FA-58AE2526FF8D(a)college-de-france.fr> > Content-Type: text/plain; charset=us-ascii > > Hi Paul, Nigel, > > Thank you for the suggestion. > > I tried to set PYTHONHOME with > export PYTHONHOME=/usr/bin/python > or > export PYTHONHOME=to PHENIX's python > or > export PYTHONHOME=to a local python compiled from source that I use to compile programs like Pymol > > to no avail, I get the same error message. > > As I can compile Rosetta without phenix using : ./scons.py -j6 mode=release bin, do you think the problem could reside in the way rosetta.build_phenix_interface works? > > Cheers, > > Ludovic. > > > On Sep 23, 2015, at 11:09 PM, Paul Adams <pdadams(a)lbl.gov> wrote: > >> Hi Ludovic, >> >> the problems seem to occur when scons is called to compile Rosetta. I notice that the scons.py file uses the python that appears first in your path (#! /usr/bin/env python). Is it possible that this is a python that is broken in some way? >> >> Cheers, >> Paul >> >>> On Sep 23, 2015, at 9:11 AM, ludovic Pecqueur <ludovic.pecqueur(a)college-de-france.fr> wrote: >>> >>> Dear Developers, >>> >>> I have a fresh Centos 7 system and after installing Phenix I wanted to compile the Rosetta.refine module. (Rosetta from source version 2015.31.58019) >>> >>> I have succesfully compiled Rosetta but when I try to build the dedicated Rosetta for Rosetta_refine with rosetta.build_phenix_interface after setting up PHENIX_ROSETTA_PATH and ROSETTA3_DB I get the following error message: >>> >>> [XXX@...]$ rosetta.build_phenix_interface nproc=6 >>> False >>> scons: Reading SConscript files ... >>> Running versioning script ... Done. (0.1 seconds) >>> Could not find platform independent libraries <prefix> >>> Could not find platform dependent libraries <exec_prefix> >>> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] >>> ImportError: No module named site >>> CalledProcessError: Command '['./update_options.sh']' returned non-zero exit status 1: >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 172: >>> main() >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConstruct", line 163: >>> SConscript("SConscript", "build") >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614: >>> return method(*args, **kw) >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 551: >>> return _SConscript(self.fs, *files, **subst_kw) >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 260: >>> exec _file_ in call_stack[-1].globals >>> File "/usr/local/PROGRAMS/ROSETTA/PHENIX_Rosetta_refine/main/source/SConscript", line 28: >>> subprocess.check_call(["./update_options.sh"]) >>> File "/usr/local/PROGRAMS/XTAL/PHENIX/phenix-1.10-2155/base/lib/python2.7/subprocess.py", line 540: >>> raise CalledProcessError(retcode, cmd). >>> >>> If you have any idea of what could cause the problem, I would welcome any suggestions. >>> I updated Phenix and I could compile phenix.rosetta_refine without problems on Centos 6.7. >>> >>> Thank you very much for your time and help. >>> >>> Kind regards, >>> >>> Ludovic. >>> >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> -- >> Paul Adams >> Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab >> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab >> Adjunct Professor, Department of Bioengineering, U.C. Berkeley >> Vice President for Technology, the Joint BioEnergy Institute >> Laboratory Research Manager, ENIGMA Science Focus Area >> >> Building 33, Room 347 >> Building 80, Room 247 >> Building 978, Room 4126 >> Tel: 1-510-486-4225, Fax: 1-510-486-5909 >> http://cci.lbl.gov/paul >> >> Lawrence Berkeley Laboratory >> 1 Cyclotron Road >> BLDG 33R0345 >> Berkeley, CA 94720, USA. >> >> Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] >> -- >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > > > ------------------------------ > > Message: 9 > Date: Mon, 28 Sep 2015 01:21:21 +0000 (UTC) > From: Smith Lee <smith_lee123(a)yahoo.com> > To: PHENIX User Mailing List <phenixbb(a)phenix-online.org> > Subject: [phenixbb] on Phenix10 > Message-ID: > <615863586.1820571.1443403281522.JavaMail.yahoo(a)mail.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > With the EM cryo data, I have compared the function of phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the Ramachandran favored, the new version is about 90%, the old version is about 92%. For the clashscore by Molprobity, the new version is about 30, the old version is about 20. Molprobity indicated the clashing atoms were systematically existing in the whole molecule, rather than on specific parts of the protein which may be indication of bad modelling. > Clearly the clashscore of 30 is unacceptable. Will you please give some advise on how to improve the function of new version of Phenix, considering adding H was not suitable as for the resolution was poorer than 4.0 A? > Smith >

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Algorithm developer postdoc opening at Berkeley National Lab
by Nicholas Sauter 28 Apr '16

28 Apr '16

Berkeley Lab's Molecular Biophysics and Integrated Bioimaging Division <http://biosciences.lbl.gov/divisions/mbib/> is looking for a Computational Biologist Postdoctoral Fellow to work in the Sauter group. We are seeking an algorithm developer for the increasingly complex analysis of large diffraction datasets in structural biology. Current projects utilize XFEL crystallography and spectroscopy to investigate the photosynthetic mechanism of water splitting and to probe other metalloenzyme reactions. We also wish to test whether diffuse scattering can reveal correlated atomic motions in crystals. Many problems remain to be solved, including the details of how to optimally merge datasets from thousands of crystals. Our software development projects (including packages such as DIALS <http://dials.lbl.gov> and cctbx.xfel <http://cci.lbl.gov/xfel>) have been highlighted in several high-impact publications listed HERE <http://biosciences.lbl.gov/profiles/nicholas-sauter>. Candidates should have expertise in one or more computational techniques including, but not limited to, ray tracing to test underlying physical models of the diffraction, Bayesian approaches for refining model parameters, macromolecular modeling and refinement, neural networks for interpreting image features, as well as signal processing and denoising methods. Extensive data analysis experience in crystallography or from more general bioimaging backgrounds are welcome. We particularly encourage strong mathematical intuition and a track record of bringing new ideas and tools to fruition, as evidenced through written publication and clear presentation. Candidates should send an expression of interest, CV, and list of three references to *Nick Sauter, nksauter(a)lbl.gov <nksauter(a)lbl.gov>.* Further details are posted at https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=82354. Nicholas K. Sauter, Ph. D. Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Rd., Bldg. 33R0345 Berkeley, CA 94720

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Weird large continuous positive density blob
by Alex Lee 26 Apr '16

26 Apr '16

Dear Phenixbb members, I have a protein (90aa length) structure with 2.3A resolution and space group P21 refined to Rfree/R to around 0.27 / 0.20. There are 3 protein dimers in one asym unit. For two dimers (chain A, B, C, D), I can see clearly continuous electron density from residue 10 to residue 89. However for the third dimer (chain E and F), I can only see clearly continuous density between residue 10 to residue 72 and lost tracing of the main chain. I did see a large electron density blob close to the third dimer. ( https://goo.gl/photos/R1SaHPKS6VLfcesb7 ; Green is positive density at 3 sigma and blue is FWT PHWT at 2sigma and 1sigma ). I do not know how to explain this blob. It seems to me that this blob is unlikely protein fragments (some parts of the blob is so chunky). Even if it's true that it's certain protein fragment between residue 73 to residue 89 of chain E or chain F, then the position of this fragment is totally different from the position of its fragment counterparts in chain A,B, C,D. I assume NCS copies (in this case maybe 3 copies) should have the same morphology as to each other. It also seems to me that this density is not from my crystal growth or harvest conditions, which has: Bis-Tris; PEG3350; PEG400 and NaCl. I do not know if Phenix Autobuild could build this automatically for me, but I'll try this later. Thanks in advance for any input on this. The density link is: https://goo.gl/photos/R1SaHPKS6VLfcesb7

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(no subject)
by Alexander Grishaev 26 Apr '16

26 Apr '16

agrishaev(a)ibbr.umd.edu

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Re: [phenixbb] Coot does not start up with OS 10.11 El Capitan
by Benoît Masquida 26 Apr '16

26 Apr '16

Following the suggestion from Engin, I indicate which installer I used to install coot, Coot-0.8.3-pre-5936_64bit_10.11.3.pkg found on Bill Scott’s website. Installation creates the following executable in the /bin directory: -rwxr-xr-x 1 root wheel 535 24 mar 17:32 coot Chown does not change solve the problem that the graphics do not appear. Any help still welcome. Best, Benoit Benoît Masquida b.masquida(a)unistra.fr UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex > Le 22 avr. 2016 à 17:40, Engin Özkan <eozkan(a)uchicago.edu> a écrit : > > As far as I know, there are no issues with Coot/Phenix on El Capitan. You may need to give more info on how you actually installed Coot (and which Coot you are invoking from Phenix, which you may have set in Coot path under Preferences->Graphics in Phenix). > Engin > > On 4/22/16 4:24 AM, Benoît Masquida wrote: >> Dear All, >> >> I re-installed Quartz as suggested. Then I have more verbose messages upon launching coot from the shell (See below). I don’t know if it is a general problem or a problem related to the configuration of my machine. >> >> Thanks. >> >> Benoit >> >> mmdcd-img2:bin B.Masquida$ ./coot >> INFO:: Reading coordinate file: /Library/Coot/share/coot/standard-residues.pdb >> PDB file /Library/Coot/share/coot/standard-residues.pdb has been read. >> Spacegroup: P 1 >> initalize graphics molecules...done. >> filter_fileselection_filenames_state () >> get_active_map_drag_flag () >> use_graphics_interface_state () >> INFO:: coot.py imported >> INFO:: coot_python initialized >> Running python script /Library/Coot/lib/python2.7/site-packages/coot/coot_load_modules.py >> Good Morning B.masquida, Welcome to Coot. 0.8.3-pre >> set_display_intro_string ("Good Morning B.masquida, Welcome to Coot. 0.8.3-pre") >> Coot Python Scripting GUI code found and loaded. >> Coot Python Scripting GUI code found and loaded. >> use_graphics_interface_state () >> filter_fileselection_filenames_state () >> get_active_map_drag_flag () >> coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. >> coot-bin: Fatal IO error 35 (Resource temporarily unavailable) on X server /private/tmp/com.apple.launchd.cTrzTueRvK/org.macosforge.xquartz:0. >> mmdcd-img2:bin B.Masquida$ >> >> >> >> >> >> Benoît Masquida >> b.masquida(a)unistra.fr <mailto:[email protected]> >> UMR 7156 GMGM >> tel: +33 3 68 85 14 81 >> fax: +33 3 68 85 13 65 >> IPCB - Plateforme de Biologie >> 4 Allée Konrad Roentgen >> 67081 STRASBOURG Cedex >> >>> Le 21 avr. 2016 à 17:10, Xiao Lei < <mailto:[email protected]>xiaoleiusc(a)gmail.com <mailto:[email protected]>> a écrit : >>> >>> Hi BM, >>> >>> If it happens after you upgrade the system, you may try re-install the Xquartz. >>> >>> On Apr 21, 2016 6:48 AM, "Benoît Masquida" <b.masquida(a)unistra.fr <mailto:[email protected]>> wrote: >>> Dear Phenix, >>> >>> The graphic window of coot does not open either launch from the shell or from Phenix GUI. Has anyone experienced (and solved) this problem on El Capitan (from Apple)? >>> >>> Thanks for your help. >>> >>> BM >>> >>> -- >>> Benoît Masquida >>> b.masquida(a)unistra.fr <mailto:[email protected]> >>> UMR 7156 GMGM >>> tel: +33 3 68 85 14 81 <tel:%2B33%203%2068%2085%2014%2081> >>> fax: +33 3 68 85 13 65 <tel:%2B33%203%2068%2085%2013%2065> >>> IPCB - Plateforme de Biologie >>> 4 Allée Konrad Roentgen >>> 67081 STRASBOURG Cedex >>> >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org <mailto:[email protected]> >>> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> >>> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb <http://phenix-online.org/mailman/listinfo/phenixbb> >> Unsubscribe: phenixbb-leave(a)phenix-online.org <mailto:[email protected]>

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Gordon Research Seminar this July
by Bradley Hintze 26 Apr '16

26 Apr '16

Attention Young scientist in crystallography and diffraction. Are you a young scientist interested in the methods in crystallography? Do you want to deepen your understanding of instrumentation, different diffraction methods, data processing, phasing, structure solution, etc.? The Gordon Research Seminar and Conference for Diffraction Methods happens July 16 - 22 (for both) at Bates College in Maine. It is a unique opportunity to interact with the researchers actively developing the exciting many methods related to crystallography and beyond. The conference is relatively small allowing close association with all in attendance allowing participants to discuss methods with those in the know. The Gordon Research Seminar is a two-day event before the Conference for those early in their career, e.g. students, postdocs, and beginning industry folks. This space allows young scientist to interact, ask questions, and discuss their science with peers. If you are interested in deepening your understanding of the methods behind crystallography, please consider applying to both the Gordon Research Seminar and Conference on Diffraction Methods. For all the details, please see: <goog_1374816820> https://www.grc.org/programs.aspx?id=16486 Apply soon! Any questions? Simply reply to this email. Thanks GRC chairs, Rike Müller-Werkmeister and Bradley Hintze

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Coot does not start up with OS 10.11 El Capitan
by Benoît Masquida 22 Apr '16

22 Apr '16

Dear Phenix, The graphic window of coot does not open either launch from the shell or from Phenix GUI. Has anyone experienced (and solved) this problem on El Capitan (from Apple)? Thanks for your help. BM -- Benoît Masquida b.masquida(a)unistra.fr UMR 7156 GMGM tel: +33 3 68 85 14 81 fax: +33 3 68 85 13 65 IPCB - Plateforme de Biologie 4 Allée Konrad Roentgen 67081 STRASBOURG Cedex

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phenix.polder - tool for calculating omit maps by excluding bulk solvent
by Dorothee Liebschner 21 Apr '16

21 Apr '16

Dear phenix users, Starting from the nightly build dev-2356, a new tool for calculating ligand omit-maps, called 'polder', is included in phenix. Usage: phenix.polder model.pdb data.mtz selection='chain A and resseq 123’ Phenix.polder calculates omit maps for atom selections by preventing the bulk solvent mask to flood into the atom selection area and its vicinity. The tool can be useful in cases where the density of the selected atoms is weak and possibly obscured by bulk solvent. Polder produces less biased maps compared to procedures where the atom selection occupancy is set to zero, and the atoms are included in the solvent mask calculation (in that case, the resulting difference density can have similar shape than the selected atoms). Phenix.polder excludes a larger volume from the bulk solvent and therefore prevents misinterpreting bulk solvent density as omit density. If you want to know more about how the tool is working and to see some examples, have a look at the presentation file: https://www.phenix-online.org/presentations/phenix_polder.pdf. The documentation page can be found here: www.phenix-online.org/version_docs/dev-2356/reference/polder.html Best wishes, Dorothee

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fit_loops using loop_lib
by Greg Bowman 21 Apr '16

21 Apr '16

Hi all - I’m having a problem getting phenix.fit_loops to run using the loop library (loop_lib=True). The phenix.fit_loops seems to work fine without this keyword (I get a good solution for a test case), but I have 3A density and wanted to restrict solutions to the loop library for the poorer density regions. I am running this from the command line, with this input: phenix.fit_loops pdb_in=refine_35-delloop1170to1172.pdb mtz_in=refine_35.mtz \ seq_file=KRJmonomer.seq start=1170 end=1172 chain_id=B \ loop_lib=True >> fit_loops-1170to1172-looplibrary.log I am using OSX ElCapitan (10.11.3) and get this error: File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 962, in <module> fit_loops=fit_loops(args=sys.argv[1:]) File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 598, in __init__ target_time=target_time, File "/Applications/phenix-1.10.1-2155/build/../modules/phenix/phenix/command_line/fit_loops.py", line 760, in run_fit target_time=target_time, File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/autosol/UserMethods.py", line 3671, in Build_fit_gaps starting_residue_number=starting_residue_number) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/loop_lib/clustering.py", line 2063, in apply_clusters d=get_density_map(map_coeffs_array=map_coeffs_array) File "/Applications/phenix-1.10.1-2155/modules/phenix/phenix/utilities/get_density_map.py", line 54, in __init__ assert not map_coeffs_array.anomalous_flag() AssertionError The last lines of the log file are: Fitting loop with loop-library... loop_lib length (including 3 on each end): 9 DATABASE: /Applications/phenix-1.10.1-2155/modules/chem_data/loop_library/loops_9_2.5/loop_lib CLUSTER_FILE: split_clusters.pkl.gz Thanks, Greg

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clash_guard failure
by Bock, Tobias 20 Apr '16

20 Apr '16

Dear colleagues, I am trying to refine a protein-DNA complex. In this structure, 2 DNA double strands are present with 50% occupancy (or similar occupancy’s) and overlap at certain positions. Phenix.refine crashed due to a nonbonded interaction distance issue. To fix that, I tried to exclude the DNA strands using: pdb_interpretation { custom_nonbonded_symmetry_exclusions="chain E" custom_nonbonded_symmetry_exclusions="chain F" } Nevertheless, phenix.refine crashed with the same error message. Changing the “nonbonded_distance_threshold” works, but results in terrible statistics (since this applies for the complete structure, I guess). Is there a way to exclude only the DNA strands (in regard to the clash guard) or a similar approach to refine the structure? Thank you in advance for your help, Tobias ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" 50 Jahre Spitzenforschung - 50 Jahre HZI: www.helmholtz-hzi.de/50 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] Merging Already-Scaled MTZs
by Tim Gruene 20 Apr '16

20 Apr '16

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Jacob, I overlooked the s at mtz, i.e. I thought you wanted to re-merge a single data set. My apologize for this. Your question is correctly formulated and perfectly valid. I would try pointless (easy) or cad (a little tedious but more prone to work) followed with aimless and its keyword 'onlymerge'. Best regards, Tim On Wednesday, April 20, 2016 07:36:07 PM you wrote: > Depends on your definition of "merge." What verb would you use for the > process I am describing? > > JPK > > -----Original Message----- > From: Tim Gruene [mailto:[email protected]] > Sent: Wednesday, April 20, 2016 3:05 PM > To: phenixbb(a)phenix-online.org > Cc: Keller, Jacob > Subject: Re: [phenixbb] Merging Already-Scaled MTZs > > Dear Jacob, > > it is technically not possible to merge relfection data twice, unless you > change to a higher symmetry space group: merging means replacing symmetry > related reflections with their mean. > > For scaling this is different - couldn't you repeat the scaling step? I am > not sure if phenix contains data processing software, I thought it starts > at data analysis and structure solution. > > Cheers, > Tim > > On Wednesday, April 20, 2016 06:59:04 PM Keller, Jacob wrote: > > Dear Crystallographers, > > > > I guess it is bad practice to merge/scale already-merged/scaled mtz's, > > but I have a special reason for wanting to do so. Does anyone know how > > this can be done in Phenix? > > > > The reason is, if you're interested, that I want to detwin several > > different datasets to varying degrees, then merge them. > > > > JPK > > > > ******************************************* > > Jacob Pearson Keller, PhD > > Looger Lab/HHMI Janelia Research Campus > > 19700 Helix Dr, Ashburn, VA 20147 > > email: kellerj(a)janelia.hhmi.org > > ******************************************* > > > > > > _______________________________________________ > > phenixbb mailing list > > phenixbb(a)phenix-online.org > > http://phenix-online.org/mailman/listinfo/phenixbb > > Unsubscribe: phenixbb-leave(a)phenix-online.org > > -- > -- > Paul Scherrer Institut > Tim Gruene > - persoenlich - > OFLC/102 > CH-5232 Villigen PSI > phone: +41 (0)56 310 5297 > > GPG Key ID = A46BEE1A - -- - -- Paul Scherrer Institut Tim Gruene - - persoenlich - OFLC/102 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v2 iD8DBQFXF9yHUxlJ7aRr7hoRArioAKDxnnJxNGZaAbV8PDmUprCJuvk7mwCg21jr wG0I05gbSvcFjrfzndkNRWY= =BHXV -----END PGP SIGNATURE-----

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Merging Already-Scaled MTZs
by Keller, Jacob 20 Apr '16

20 Apr '16

Dear Crystallographers, I guess it is bad practice to merge/scale already-merged/scaled mtz's, but I have a special reason for wanting to do so. Does anyone know how this can be done in Phenix? The reason is, if you're interested, that I want to detwin several different datasets to varying degrees, then merge them. JPK ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kellerj(a)janelia.hhmi.org *******************************************

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Autobuild
by Sam Tang 20 Apr '16

20 Apr '16

Dear colleagues I have recently downloaded a Windows GUI version of Phenix 1.10.1-2155. When I used AutoBuild these few days it keeps turning out the following errors: Job 1 failed: child process stderr output: command: ['phenix.autobuild', 'C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\PARAMS_1.eff', 'write_run_directory_to_file="C:\\Users\\pcshaw\\Desktop\\NPAproc\\B13_proc\\AutoBuild_run_4_\\TEMP0\\INFO_FILE_1"'] Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\build\..\modules\phenix\phenix/command_line\autobuild.py", line 228, in <module> run_autobuild=run_autobuild(args=sys.argv[1:]) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 564, in __init__ self.RunWizard() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 1001, in RunWizard self.runWizard.run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\wizard_command_line.py", line 137, in run self.Wizard.Run(info='script') File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 836, in Run self.DoNextMethod() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 1004, in DoNextMethod raise AssertionError, line AssertionError: Traceback (most recent call last): File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 987, in DoNextMethod self.CarryOutBest() # to be obtained after it is finished File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\autosol\AutoBaseExtend.py", line 2147, in CarryOutBest getattr(self,str(self.application_method))() # call this fn File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 2372, in AutoBuild_build_cycle self.AutoBuild_rebuild_cycle_run() File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 4626, in AutoBuild_rebuild_cycle_run refine_2fofc=refine_2fofc) File "C:\Program Files\Phenix\phenix-installer-1.10.1-2155-win7vc90\modules\phenix\phenix\wizards\AutoBuild.py", line 5500, in AutoBuild_resolve_with_model hklout=hklout,labin=labin) UnboundLocalError: local variable 'labin' referenced before assignment Could I please enquire if these are due to mis-setting of parameters or in fact problems related to my recent installation? Yet another question on my mind is, is AutoMR still supported in this Windows version? I can now no longer find it in the GUI while it used to be there in the 1.7 Mac version. Kind regards Sam Biochemistry Programme, School of Life Sciences, CUHK

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phenix output graphs
by Christian Roth 19 Apr '16

19 Apr '16

Hi Phenix-Team, there are some nice graphs produced for example after refinement. If I want to save such a graph (B-Factor histogram) as jpg or so, is that possible or do I have to save the values and redraw it outside phenix? The only plot I oculd save was the B-Fac plot per residue, which wouldn't be helpful in that case. Thanks for some insight. Cheers Christian

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questions/problems with tls_as_xyz routines
by David A Case 18 Apr '16

18 Apr '16

I'm trying to use tls_as_xyz, but having some problems. 1. In the paper describing this, Urzhumtsev et al, Acta Cryst D71:1668, 2015, there seems to be something wrong with Section 6.2, which describes results on PDB entry "1dqv", syanptotagmin III. The description says that there are two copies of the molecule in the asymmetric unit, and the resolution is 2.5 Ang. However, the file with this code in the RCSB (which is indeed syanptotagmin III) has one molecule per asymmetric unit, a single chain of 296 amino acids, rather than two chains of 97 amino acids, as in Tables 2 and 3 of the paper cited above; the resolution is 3.2 Ang. And it doesn't look anything like the picture of "1dqv" in Fig. 3a. So something looks wrong; does anyone know what system Section 6.2 is using? 2. I'm asking the above because I'm having trouble with my own applications, and was hoping to check that I could reproduce the results in the paper. Apropos of that, is there a test case or example for tls_as_xyz in the phenix distribution? [I'm not all that familiar with phenix, so apologies if I've missed the easy way to find this.] 3. Here is a summary of what is not working for me. (I don't expect anyone to debug this on such little information, but thought that someone on the list might have done some similar calculation.) a. I took a small domain (residues 6-61 from GB3, PDB code 2IGD), and used Ethan Merrit's lsq_tls_fit to obtain a set of TLS tensors that best fit the deposited ADP's. The statisitcs are pretty good, indicating (not surprisingly) that motions in this domain are well characterized as a rigid body--which is why I chose this system. I just used the CA atoms for this initial study. b. I used phenix.tls_as_xyz to compute an ensemble from the TLS matrices obtained in step a. c. I then computed ADP's from the ensemble, using tools from cpptraj in Amber, (or our own codes, which give the same results). But the extracted isotropic B factors (and the anisotropic components) are much larger than the input ones. So, the ensemble is giving me what I expected: a sampling of structures whose fluctuations arise from the input TLS matrices. I've done a fair amount of due diligence in trying to track down errors on my end, but I could be making a mistake on any one of the steps above. Or, I could be mis-interpreting what I should expect to get from the tls_as_xyz procedure. I'd be happy to share details off-line with any one who might volunteer to help. ...thanks...dave case

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Application deadline is this week: CCP4/APS crystallographic school, June 21 - 29, 2016
by Sanishvili, Ruslan 18 Apr '16

18 Apr '16

Dear Colleagues, Deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. If you have a crystallographic problem you cannot resolve independently, this school is for you. From our past experience, the majority of participants bring with them the crystallographic problems and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed at http://www.ccp4.ac.uk/schools/APS-school/publications.php This school will cover popular packages such as CCP4, PHENIX, SHELX and much, much more: http://www.ccp4.ac.uk/schools/APS-2016/program.php Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found at: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Wednesday, March 23, 2016 10:26 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] Reminder, CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, This is a reminder that the application deadline for the 9th annual CCP4/APS crystallographic school is on April 21, 2016. Applications received after this date will not be considered. The school will take place from June 21 through June 29, 2016 at the Advanced Photon Source, Argonne National Laboratory, near Chicago. All aspects of macromolecular crystallography from data collection to structure refinement and validation, as well as functional assessment, will be covered. Instructions and hands-on assistance will be provided by the authors and developers of the represented software, and/or by other premier experts. >From our past experience, the majority of participants bring with them the crystallographic problems they cannot resolve independently and almost all these problems are resolved at the school. Some of the publications, acknowledging the contribution of the school, are listed here: http://www.ccp4.ac.uk/schools/APS-school/publications.php Each registered participant will be provided with a Linux computer with all covered software already installed and configured. Lodging is on-campus and all meals and refreshments will be provided at the venue. These and other details, such as the fees, the on-line application, the program, the contact information etc. can be found here: http://www.ccp4.ac.uk/schools/APS-2016/index.php We are looking forward to meeting you in Argonne this summer. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov ________________________________ From: phenixbb-bounces(a)phenix-online.org [phenixbb-bounces(a)phenix-online.org] on behalf of Sanishvili, Ruslan [rsanishvili(a)anl.gov] Sent: Tuesday, February 23, 2016 7:48 AM To: phenixbb(a)phenix-online.org Subject: [phenixbb] CCP4 crystallographic summer school at the APS, June 21 - 29, 2016 Dear Colleagues, We are pleased to announce the 9th annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Title: CCP4 crystallographic school: From data collection to structure refinement and beyond Dates: June 21 through 29, 2016 Site: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA The school comprises Data collection workshop the first three days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Crystallographic computation workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on, interactive trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level, along with commercial/industrial researchers are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. Application: Application deadline is April 21. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2016/index.php Registration fees: The registration fee for the selected participants is $400 for the academic and $950 for the industrial researchers. The link for the on-line payments and instructions will be provided once the selection process is completed. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making the reservations at economical lodging at the Argonne Guest House. The workshop will cover all other expenses. We hope to see you at the school, Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Lemont, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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Re: [phenixbb] Data processing: exhaustive search?
by Kay Diederichs 17 Apr '16

17 Apr '16

Hi Kaushik, there is no need for, and no sense in, an exhaustive search of data processing parameter space, because its dimensionality is way too high to achieve anything useful. The programs MOSFLM and XDS have undergone decades of development, and their processing defaults are carefully chosen. It is rather the user of the programs who is in charge to correctly interpret the output (which requires reading of their documentation, and some experience), and to make meaningful adjustments to (usually very) few parameters. Speaking for XDS, I recommend to read XDSwiki articles (there are tutorials and example data sets, and lots of explanations) and a book chapter that I recently wrote (#131 at http://cms.uni-konstanz.de/strucbio/diederichs-group/publications ). If you use the generate_XDS.INP script from XDSwiki, and follow the paper and the "Optimization" article, you will get good data from XDS. (There are other scripts, like autoPROC, xia2, xdsme and so on, which usually also give good results but I don't know them well.) In particular, in case of XDS there is usually no need to fiddle around with "box size, spot separation, tolerance and other parameters". The fact that you seem to try and optimize Rmerge suggests to me that you are trading precision for accuracy. Too many people still do this, but it is a legacy of the past. "Trying a combination of better frames over poorer frames" is most likely _not_ going to improve your merged intensities - this is another unfortunate and very common misunderstanding (see references 113 and 130). I hope this helps you to get better data. Kay On 16.04.2016 21:18, phenixbb-request(a)phenix-online.org wrote: > Message: 6 > Date: Sun, 17 Apr 2016 00:48:31 +0530 > From: Kaushik Hatti <hskaushik(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Data processing: exhaustive search? > Message-ID: > <CAGMFGb=B9s-j4yXmRx8_M7NPndf86puviiY9QMg=EAqaWr9thw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data > is not of great quality with very close spots, ellipsoid spots in certain > regions of the frames and spot overlaps. Also certain frames are poorer > than rest. The crystal could not be reproduced. > > The best R merge (overall) I have achieved so far is 17% with 85% > completeness and 3 I/SigI processed in P4 space group. I feel it's possible > to process it better by identifying right values for box size, spot > separation, tolerance and other parameters. I am also suspecting a higher > symmetry space group. I believe, trying a combination of better frames > over poorer ones with improve merging statistics. > > I have so far tried processing in iMosflm and XDS. Is there a tool which > could search exhaustively trying different values for parameters and > suggest the combination which provide best merging statistics? > > Sorry if this question is not relevant in this group. > Any pointers/suggestions would be gratefully helpful. > > Thanks in advance, > Regards, > Kaushik > Molecular Biophysics Unit, > Indian Institute of Science, > Bangalore, India. -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz

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Data processing: exhaustive search?
by Kaushik Hatti 16 Apr '16

16 Apr '16

Hello, I have a data set diffracted to 2.7A collected at 1.54 wavelength. The data is not of great quality with very close spots, ellipsoid spots in certain regions of the frames and spot overlaps. Also certain frames are poorer than rest. The crystal could not be reproduced. The best R merge (overall) I have achieved so far is 17% with 85% completeness and 3 I/SigI processed in P4 space group. I feel it's possible to process it better by identifying right values for box size, spot separation, tolerance and other parameters. I am also suspecting a higher symmetry space group. I believe, trying a combination of better frames over poorer ones with improve merging statistics. I have so far tried processing in iMosflm and XDS. Is there a tool which could search exhaustively trying different values for parameters and suggest the combination which provide best merging statistics? Sorry if this question is not relevant in this group. Any pointers/suggestions would be gratefully helpful. Thanks in advance, Regards, Kaushik Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

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Re: [phenixbb] Hardward phenix.refine
by Kay Diederichs 12 Apr '16

12 Apr '16

Colin, check out the first option in the FAQ at https://www.phenix-online.org/documentation/faqs/refine.html A core i7 and a Xeon of the same generation are equally fast if their frequency is the same. The main differences are that - Xeon E3 supports ECC memory (most core i* don't) - Xeon E5 supports Dual-CPU (core i* is just one) - Xeon E7 supports multi-CPU and is very expensive - most Xeons don't have built-in graphics whereas most core i* do There are many other small differences but most of them irrelevant; inspect the Wikipedia pages! Xeons won't be faster with phenix.refine; a core i7 already has enough cores - to increase their usage you'll have to recompile as per the FAQ. HTH, Kay > > Message: 1 > Date: Mon, 11 Apr 2016 07:56:39 +0000 > From: Colin Levy <C.Levy(a)manchester.ac.uk> > To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Hardward phenix.refine > Message-ID: <773C4580-FA01-4246-86E9-2D73AFD98421(a)manchester.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > Having read the FAQ regarding hardware I have a few ideas but would greatly appreciate any input from the community or developers. > > Would anyone like to suggest the best configuration of hardware for running phenix.refine? I mainly operate in OSX but have no issue with switching operating system if I can get a faster setup. My current thoughts are either something running a 4GHz Quad core i7 or an alternative would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent Linux builds. > > I know that the i7 is reasonably fast as I have this setup in a different machine and phenix.refine runs reasonably quickly but as ever I would like it to be faster. Budget is not unlimited by any means but I would be interested in learning what an optimal setup might look like. > > Many thanks, > > Colin > > > Manchester > Protein > Structure > Facility > > 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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