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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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