- phenixbb - phenix-online.org

ISOLDE 1.0b2 release
by Tristan Croll 25 Jan '19

25 Jan '19

Dear structural biology community, I am very happy to announce that ISOLDE 1.0b2 is now available. All the details including documentation are available on the new ISOLDE website at https://isolde.cimr.cam.ac.uk, but the following is a short list of new features and improvements since ISOLDE 1.0b1: - added support for Windows. ISOLDE is now available for all three major operating systems. - many usability and stability improvements. In particular, ISOLDE is now much more helpful when your starting model is not yet quite simulation-ready. - No more need to delete unparameterised residues from your model. You can now choose to have ISOLDE simply ignore them for simulation purposes. - Real-time smoothing of the trajectory visualisation to reduce thermal jitter. - Direct handling of real-space maps (no need to convert them to structure factors first). - Live recalculation of structure factors and crystallographic maps from F/sigF data as model coordinates change. I do hope you find it useful. Best regards, Tristan

1 1

(IUCr) Iron–sulfur clusters have no right angles
by Edward A. Berry 16 Jan '19

16 Jan '19

Iron–sulfur clusters have no right angles Nigel W. Moriarty and Paul D. Adams, Acta Cryst. (2019). D75, 16–20 <http://journals.iucr.org/d/issues/2019/01/00/rr5165/index.html> This agrees well with what we see in structures of respiratory complex II! But when I downloaded geostd.tar from https://sourceforge.net/projects/geostd/ and look in SF4.cif, I see: SF4 SF4 'Iron/sulfur cluster' Ion/Group/Compound 8 8 . 2009-09-01 2009-09-01 ~~~~ loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd SF4 FE3 S2 FE1 90.000 3.000 SF4 FE4 S2 FE1 90.000 3.000 SF4 FE2 S3 FE1 90.000 3.000 SF4 FE4 S3 FE1 90.000 3.000 SF4 FE2 S4 FE1 90.000 3.000 ~~~~ SF4 S3 FE2 S1 90.000 3.000 SF4 S4 FE2 S1 90.000 3.000 SF4 S2 FE3 S1 90.000 3.000 SF4 S4 FE3 S1 90.000 3.000 SF4 S2 FE4 S1 90.000 3.000 SF4 S3 FE4 S1 90.000 3.000 SF4 S3 FE1 S2 90.000 3.000 Did I get an outdated version?

2 3

Postdoctoral position at UW-Madison
by Eric Montemayor 15 Jan '19

15 Jan '19

A postdoctoral position is immediately available in the laboratory of Professor Samuel Butcher at the University of Wisconsin-Madison. https://biochem.wisc.edu/faculty/butcher The Butcher laboratory is funded by the NIH to investigate the structure and function of RNA-protein complexes that regulate gene expression. Additionally, the lab is currently determining structure activity relationships for small molecules that regulate non-coding RNAs that play roles in neurodegenerative diseases. The Butcher laboratory is part of a vibrant research community at UW-Madison with state-of-the-art resources, such as the National Magnetic Resonance Facility at Madison (NMRFAM) and a newly established cryo-EM facility that will soon house a Titan Krios, Talos Arctica and Aquilos FIB/SEM electron microscope. The Butcher laboratory has established expertise in NMR, X-ray crystallography, SAXS, and myriad biophysical techniques. Additionally, we collaborate with local experts in cryo-electron microscopy. Thus, postdoctoral trainees in the Butcher lab are in a position to learn any aspect of contemporary structural biology. Recent publications: www.ncbi.nlm.nih.gov/pubmed/30215753 www.ncbi.nlm.nih.gov/pubmed/29717126 www.ncbi.nlm.nih.gov/pubmed/28887445 www.ncbi.nlm.nih.gov/pubmed/27194769 www.ncbi.nlm.nih.gov/pubmed/26655855 www.ncbi.nlm.nih.gov/pubmed/24837192 Requirements are a PhD in biochemistry or related scientific field. If interested, please send CV by email to: sebutcher(a)wisc.edu

1 0

Refining an ion on a special position
by Shane Caldwell 12 Jan '19

12 Jan '19

Hi phenixbb, I've got a question related to refinement of an ion on a special position. I have a structure with an atom placed squarely on the C2 axis. I've been able to get a mostly-reasonable model by dropping in the ion at 0.5 occupancy and turning off repulsion for the ion in question, as Pavel describes here <http://www.phenix-online.org/pipermail/phenixbb/2018-February/023689.html>. It almost completely works. The thing I find now is that during refinement there can still be some random drift of the atom away from the symmetry axis, splitting from its symmetry ghost, while I know that it should stay perfectly coincident. My resolution is 3.1 and there's no indication of a multiple conformation, so a split isn't justified. The most parsimonious model should place the ion exactly on the C2. Is there any way to enforce that either 1. x, y = 0.0 in refinement, or 2. the ion is constrained to the xyz of the symmetric version of itself. Both should get to the same place, with the metal precisely on the axis, and precisely over top of it's symmetric counterpart. Thanks! Shane Caldwell Senior Fellow, Institute for Protein Design University of Washington Seattle, WA scald(a)uw.edu shane.caldwell17(a)gmail.com

3 5

atoms with unknown nonbonded energy type
by Danilo Belviso 12 Jan '19

12 Jan '19

Dear all, I am refining the structure of a cyclic peptide with having residues that are not in the ligand list of phenix. I would to perform unrestrained refinement by considering the very good resolution of the data. However, also in this case, phenix requires the restrain file of the ligand. I got cif file in two different way: 1) PRODRG server 2) by running phenix.elbow both produce the restrain file with no error message. However, by using such file in the refining, I get this error: Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 14 In the cif file, there are not atoms having 14 as energy type symbols. Could you suggest to what this message is referred to? How can I modify the cif to overcome the problem? Thanks in advance, Danilo -- Dr. Belviso Benny Danilo, PhD Istituto di Cristallografia (IC) Consiglio Nazionale delle Ricerche (CNR) via Amendola 122/o, 70126 Bari - Italy Tel ++39 080 5929273 Fax ++39 080 5929170 mail: danilo.belviso(a)ic.cnr.it web: users.ba.cnr.it/ic/crisdb00

2 1

Re: [phenixbb] Phenix installation on Debian9.6
by Billy Poon 10 Jan '19

10 Jan '19

Hi Danilo, I have a Debian 9.6 virtual machine running and Phenix is working after en_GB is installed. The problem is with the locale. It looks like en_GB is required even though another language is used. I had to install en_GB even if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB error. After installing en_GB, the GUI works normally (see attached screenshot, phenix.png). To install en_GB with instructions from https://wiki.debian.org/Locale, 1) open a Terminal and become root 2) run "dpkg-reconfigure locales" 3) Select en_GB.UTF-8 (see attached screenshot, locale.png) 4) Select "OK" and complete process. You'll have to just choose your default language, but you should have it_IT.UTF-8 as your default 5) Verify that en_GB is available with "locale -a" (Mine is shown in a terminal in phenix.png) Changing the setting for Phenix 1) Go to the <phenix installation>/build directory 2) Type "export LC_ALL=it_IT.UTF-8" 3) Run the config_modules.sh script 4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I check that <phenix installation>/build/bin/phenix has LC_ALL set to it_IT.UTF-8 5) Phenix should run and the main GUI should pop up I suspect that because Phenix is not localized, we may be requiring an English language to be installed and maybe en_GB is a default. So in phenix.png, the dates for the projects are in Italian, but everything else is in English. Also, I think our number formatting is not localized, so decimal points will be "." instead of ",". I'm sending the images to you directly since the bulletin board has some size limit and the original message with attached images is waiting approval. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org On Wed, Jan 9, 2019 at 8:53 AM Billy Poon <BKPoon(a)lbl.gov> wrote: > Hi Danilo, > > I have a Debian 9.6 virtual machine running and Phenix is working after > en_GB is installed. The problem is with the locale. It looks like en_GB is > required even though another language is used. I had to install en_GB even > if I'm using en_US. When I have only it_IT.UTF-8 installed, I get the en_GB > error. After installing en_GB, the GUI works normally (see attached > screenshot, phenix.png). > > To install en_GB with instructions from https://wiki.debian.org/Locale, > 1) open a Terminal and become root > 2) run "dpkg-reconfigure locales" > 3) Select en_GB.UTF-8 (see attached screenshot, locale.png) > 4) Select "OK" and complete process. You'll have to just choose your > default language, but you should have it_IT.UTF-8 as your default > 5) Verify that en_GB is available with "locale -a" (Mine is shown in a > terminal in phenix.png) > > Changing the setting for Phenix > 1) Go to the <phenix installation>/build directory > 2) Type "export LC_ALL=it_IT.UTF-8" > 3) Run the config_modules.sh script > 4) Verify that "LC_ALL=it_IT.UTF-8" is in our programs. In phenix.png, I > check that <phenix installation>/build/bin/phenix has LC_ALL set to > it_IT.UTF-8 > 5) Phenix should run and the main GUI should pop up > > I suspect that because Phenix is not localized, we may be requiring an > English language to be installed and maybe en_GB is a default. So in > phenix.png, the dates for the projects are in Italian, but everything else > is in English. Also, I think our number formatting is not localized, so > decimal points will be "." instead of ",". > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org > > > On Wed, Jan 9, 2019 at 12:32 AM Tim Gruene <tim.gruene(a)psi.ch> wrote: > >> Dear Danilo, >> >> I agree that the language settings are probably not the cause of the >> problem. >> >> Maybe phenix created a segmentation fault. On recent versions of Debian, >> these >> show in the output of dmesg, but not necessarily in the terminal where >> you >> started phenix. >> >> Run phenix again, then type 'dmesg -T' to check if there is a >> segmentation >> fault. >> >> Best, >> Tim >> >> >> On Wednesday, January 9, 2019 9:15:39 AM CET Danilo Belviso wrote: >> > Dear Billy K. Poon, >> > >> > Thanks for your suggestion. My LANG variable is it_IT.UTF-8 and LC_ALL >> > in /build/bin/phenix is en_US.UTF-8. Unfortunately, once changed the >> > variable, reconfiguration as suggested doesn't fix up the problem. I >> > would like to say that the problem/warning related to "locale 'en_GB' >> > cannot be set" is just one of that shown in my first email. Likely, it >> > is also the less important. Indeed, I always had the same problem with >> > previous versions of phenix. The difference is that in that case phenix >> > worked and now it stops abruptly. It is just my opinion but the problem >> > could be in the list I posted in the first email. >> > >> > Thanks again for your suggestions. >> > >> > Regards, >> > >> > Danilo >> > >> > Il 2019-01-08 17:16 Billy Poon ha scritto: >> > > Hi Danilo, >> > > >> > > Another user on Debian 9 had a similar issue. What is the output to >> > > "locale -a" and what is your LANG and LC_ALL environment variables set >> > > to? And in the <phenix installation>/build/bin/phenix file, there is a >> > > place where LC_ALL is set. What is LC_ALL set to in that file? >> > > >> > > For unicode support, Phenix requires a language with UTF8 support >> > > (e.g. en_GB.UTF-8). During the installation, Phenix tries to determine >> > > the locale from the LC_ALL environment variable. By default, it gets >> > > set to en_US.UTF-8 if nothing can be found. However, on Debian 9, I >> > > got an error about en_GB even though en_US was available and set as >> > > the locale. >> > > >> > > On my Debian 9.6 virtual machine, I have en_US.UTF-8 and en_GB.UTF-8 >> > > installed and my phenix installation is using en_US.UTF-8. If you want >> > > to update the LC_ALL variable in the scripts in <phenix >> > > installation>/build/bin, >> > > >> > > 1) Set LC_ALL to the language you want with UTF-8 support (e.g. >> > > "export LC_ALL=en_US.UTF-8") >> > > 2) Run the "config_modules.sh" file in the <phenix installation>/build >> > > directory to change all the scripts to use the new locale. >> > > >> > > -- >> > > Billy K. Poon >> > > >> > > Research Scientist, Molecular Biophysics and Integrated Bioimaging >> > > Lawrence Berkeley National Laboratory >> > > 1 Cyclotron Road, M/S 33R0345 >> > > Berkeley, CA 94720 >> > > Tel: (510) 486-5709 >> > > Fax: (510) 486-5909 >> > > Web: https://phenix-online.org >> > > >> > > On Tue, Jan 8, 2019 at 7:47 AM Danilo Belviso >> > > >> > > <danilo.belviso(a)ic.cnr.it> wrote: >> > >> Dear Rob, >> > >> >> > >> Thanks for your suggestions. I have just tried but it doesn't work, >> > >> unfortunately. >> > >> >> > >> Thanks again. >> > >> >> > >> Regards, >> > >> >> > >> Danilo >> > >> >> > >> Il 2019-01-08 15:43 Robert Oeffner ha scritto: >> > >>> Dear Danilo, >> > >>> >> > >>> >> > >>> I encountered the same problem with the locale when installing >> > >> >> > >> Phenix >> > >> >> > >>> on Ubuntu on Windows 10. The solution was to do from a bash shell: >> > >>> >> > >>> >> > >>> *cd /usr/share/locale* >> > >>> >> > >>> ** >> > >>> >> > >>> *sudo locale-gen "en_GB.UTF-8"* >> > >>> >> > >>> ** >> > >>> >> > >>> *sudo dpkg-reconfigure locales* >> > >>> >> > >>> I'm no linux expert so I wouldn't know if this procedure is >> > >> >> > >> general >> > >> >> > >>> enough that it would work on your system or if it would also solve >> > >> >> > >> the >> > >> >> > >>> other issues you mention before. >> > >>> >> > >>> Regards, >> > >>> >> > >>> Rob >> > >>> >> > >>> On 08/01/2019 14:32, Danilo Belviso wrote: >> > >>>> Dear all, >> > >>>> >> > >>>> I am intalling phenix on my Debian 9.6. >> > >>>> >> > >>>> My arch is adm64 thus I downloaded the phenix version named >> > >> >> > >> Kernel 2.6 >> > >> >> > >>>> (64-bit; CentOS 6). >> > >>>> >> > >>>> The installation procedure has been performed as suggested by the >> > >>>> >> > >>>> guide and no problems were obtained. However, by running phenix >> > >> >> > >> (after >> > >> >> > >>>> source phenix_env.sh) I get the follow output with several >> > >> >> > >> errors: >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: >> > >> assertion >> > >> >> > >>>> 'G_IS_LOADABLE_ICON (icon)' failed >> > >>>> (main.py:14196): Gtk-WARNING **: Error loading theme icon >> > >> >> > >> 'gtk-ok' for >> > >> >> > >>>> stock: Failed to load icon >> > >> >> > >>>> (main.py:14196): Gtk-CRITICAL **: render_fallback_image: >> > >> assertion >> > >> >> > >>>> 'pixbuf != NULL' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >> >> > >>>> (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: >> > >> assertion >> > >> >> > >>>> 'G_IS_OBJECT (object)' failed >> > >>>> >> > >>>> Error in sys.excepthook: >> > >>>> Traceback (most recent call last): >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 886, in _excepthook >> > >>>> Error.show_exception_dialog(type, value, traceback) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Error.py" >> > > , >> > > >> > >>>> line 75, in show_exception_dialog >> > >>>> if (app.bug_timer.IsRunning() is False): >> > >>>> AttributeError: 'PhenixApp' object has no attribute 'bug_timer' >> > >>>> >> > >>>> Original exception was: >> > >>>> Traceback (most recent call last): >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/ >> > > command_line/main.py",> >> > >>>> line 23, in <module> >> > >>>> run(sys.argv[1:]) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/ >> > > command_line/main.py",> >> > >>>> line 17, in run >> > >>>> wxapp = App.PhenixApp(args) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 70, in __init__ >> > >>>> wx.App.__init__(self, 0) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-package >> > > s/wx-3.0-gtk2/wx/_core.py",> >> > >>>> line 8628, in __init__ >> > >>>> self._BootstrapApp() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-package >> > > s/wx-3.0-gtk2/wx/_core.py",> >> > >>>> line 8196, in _BootstrapApp >> > >>>> return _core_.PyApp__BootstrapApp(*args, **kwargs) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 116, in OnInit >> > >>>> self.start_gui() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", >> > > >> > >>>> line 144, in start_gui >> > >>>> callback_on_import=self.show_message) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 280, in start_tracking >> > >>>> project_class="wxGUI2.Tracking.phenix_project_database", >> > >> >> > >> **kwds) >> > >> >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > __init__.py",> >> > >>>> line 19, in start_tracking >> > >>>> callback_on_import=callback_on_import) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 117, in __init__ >> > >>>> super(phenix_project_database, self).__init__(*args, **kwds) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > project_db.py",> >> > >>>> line 39, in __init__ >> > >>>> self.choose_project(try_current_dir=True) >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/ >> > > project_db.py",> >> > >>>> line 339, in choose_project >> > >>>> project_info = self.create_first_project() >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking. >> > > py",> >> > >>>> line 124, in create_first_project >> > >>>> from wxGUI2.Home import Projects >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Home/Proj >> > > ects.py",> >> > >>>> line 3, in <module> >> > >>>> from wxGUI2 import Base, Controls, PhilLayout, Windows, >> > >> >> > >> utils, >> > >> >> > >>>> Buttons >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/PhilLayou >> > > t.py",> >> > >>>> line 5, in <module> >> > >>>> from wxGUI2 import Base, Controls, Windows, utils, >> > >> >> > >> PhilInterface, >> > >> >> > >>>> FileDisplay >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/FileDispl >> > > ay.py",> >> > >>>> line 5, in <module> >> > >>>> import wxtbx.info_panels >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/inf >> > > o_panels.py",> >> > >>>> line 5, in <module> >> > >>>> import wxtbx.plots >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plo >> > > ts/__init__.py",> >> > >>>> line 21, in <module> >> > >>>> locale.setlocale(locale.LC_ALL, '') >> > >>>> File >> > > >> > > >> "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/locale.py", >> > > >> > >>>> line 581, in setlocale >> > >>>> return _setlocale(category, locale) >> > >>>> locale.Error: unsupported locale setting >> > >>>> >> > >>>> >> > >>>> >> > >>>> Phenix starts by opening a window that states "locale 'en_GB' >> > >> >> > >> cannot >> > >> >> > >>>> be set" and abruptly closes so that I cannot use it. >> > >>>> >> > >>>> Do you have any suggestions to overcome such problems? >> > >>>> >> > >>>> I tried with Kernel 2.6 (64-bit; CentOS 5) and the 32-bit version >> > >> >> > >> too >> > >> >> > >>>> and the result is the same. >> > >>>> >> > >>>> Thanks in advance for your suggestions. >> > >>>> >> > >>>> Danilo >> > >>>> _______________________________________________ >> > >>>> phenixbb mailing list >> > >>>> phenixbb(a)phenix-online.org >> > >>>> http://phenix-online.org/mailman/listinfo/phenixbb >> > >>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> > >> >> > >> _______________________________________________ >> > >> phenixbb mailing list >> > >> phenixbb(a)phenix-online.org >> > >> http://phenix-online.org/mailman/listinfo/phenixbb >> > >> Unsubscribe: phenixbb-leave(a)phenix-online.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 - >> OSUA/204 >> Forschungsstrasse 111 >> CH-5232 Villigen PSI >> phone: +41 (0)56 310 5297 >> >> GPG Key ID = A46BEE1A >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > >

1 0

Phenix installation on Debian9.6
by Danilo Belviso 09 Jan '19

09 Jan '19

Dear all, I am intalling phenix on my Debian 9.6. My arch is adm64 thus I downloaded the phenix version named Kernel 2.6 (64-bit; CentOS 6). The installation procedure has been performed as suggested by the guide and no problems were obtained. However, by running phenix (after source phenix_env.sh) I get the follow output with several errors: (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GIO-CRITICAL **: g_loadable_icon_load: assertion 'G_IS_LOADABLE_ICON (icon)' failed (main.py:14196): Gtk-WARNING **: Error loading theme icon 'gtk-ok' for stock: Failed to load icon (main.py:14196): Gtk-CRITICAL **: render_fallback_image: assertion 'pixbuf != NULL' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_ref: assertion 'G_IS_OBJECT (object)' failed (main.py:14196): GLib-GObject-CRITICAL **: g_object_unref: assertion 'G_IS_OBJECT (object)' failed Error in sys.excepthook: Traceback (most recent call last): File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 886, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Error.py", line 75, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/home/bbdanilo/Programmi/phenix-1.14-3260/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 70, in __init__ wx.App.__init__(self, 0) File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 116, in OnInit self.start_gui() File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/App.py", line 144, in start_gui callback_on_import=self.show_message) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 280, in start_tracking project_class="wxGUI2.Tracking.phenix_project_database", **kwds) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/__init__.py", line 19, in start_tracking callback_on_import=callback_on_import) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 117, in __init__ super(phenix_project_database, self).__init__(*args, **kwds) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py", line 39, in __init__ self.choose_project(try_current_dir=True) File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/phenix/tracking/project_db.py", line 339, in choose_project project_info = self.create_first_project() File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Tracking.py", line 124, in create_first_project from wxGUI2.Home import Projects File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/Home/Projects.py", line 3, in <module> from wxGUI2 import Base, Controls, PhilLayout, Windows, utils, Buttons File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/PhilLayout.py", line 5, in <module> from wxGUI2 import Base, Controls, Windows, utils, PhilInterface, FileDisplay File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/phenix/wxGUI2/FileDisplay.py", line 5, in <module> import wxtbx.info_panels File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/info_panels.py", line 5, in <module> import wxtbx.plots File "/home/bbdanilo/Programmi/phenix-1.14-3260/modules/cctbx_project/wxtbx/plots/__init__.py", line 21, in <module> locale.setlocale(locale.LC_ALL, '') File "/home/bbdanilo/Programmi/phenix-1.14-3260/base/lib/python2.7/locale.py", line 581, in setlocale return _setlocale(category, locale) locale.Error: unsupported locale setting Phenix starts by opening a window that states "locale 'en_GB' cannot be set" and abruptly closes so that I cannot use it. Do you have any suggestions to overcome such problems? I tried with Kernel 2.6 (64-bit; CentOS 5) and the 32-bit version too and the result is the same. Thanks in advance for your suggestions. Danilo

4 5

Jumping Rfree upon bulk solvent modeling
by Weinert Tobias (PSI) 09 Jan '19

09 Jan '19

Dear PHENIXBB community, i have come across a strange behavior in Phenix: * I copied Rfree-flags from a dataset with very slightly different unit cell * Refined the previously refined model against the new data * Rfactors in first round were good * Second round in refinement Rfree was up by 10 % just from the start during bulk solvent modeling and scaling * In another round Rfree was high in the beginning, and then dropped by those 10 % during bulk solvent modelling and scaling. * In yet another round Rfree started 10% lower than the previous round during bulk solvent modeling in the first cycle and then it jumps up again in the second cycle. What could be wrong? Many thanks and kind regards, Tobias Weinert

2 1

mmCIF in Phenix 1.14-3260
by Dominik Oberthuer 31 Dec '18

31 Dec '18

Dear all, I recently found that phenix.refine in version 1.14-3260 generates coordinate mmCIFs that the PDB deposition system can't handle. After struggling with this for some time I used an installation of Phenix 1.13-2998 I still have on my MacBook and used the mmCIF/PDB-conversion tool from this version and had no more trouble with uploading the mmCIF to the PDB. Maybe it is worthwhile to check which changes from 1.13 to 1.14 might have caused these issues. Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

5 11

smaller the cell parameter of EM map
by dancingdream＠163.com 30 Dec '18

30 Dec '18

Dear all, The cell parameter of the EM map is always too large, which will make the model building program running very slow. But in factor, the structure is a smal part of cell. So can I smaller the cell parameter when I use phenix.map_to_structure_factors to convert the EM map to mtz file. Thank a lot! Wei

2 4