- phenixbb - phenix-online.org

Exclude Waters from order_solvent=true updates
by Schulz, Dr. Eike 13 Nov '23

13 Nov '23

Hello everyone, I am refining a few structures via a bash script using constrained occupancy refinement by providing a parameter file. I am trying to model the occupancy of a ligand and the water molecules in its vicinity. This works generally well, but as soon as I switch on ordered_solvent=true, these water molecules are also filtered / updated and eventually removed. How can I avoid this ? That is specifically excluding a number of water molecules from being updated ? With best regards, Eike

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Automated estimation of voxel size using reference pixel size in phenix?
by Oliver Clarke 13 Nov '23

13 Nov '23

Hi, In cryoEM, the pixel size is often not known with certainty, and we need to calibrate it by measuring the real space correlation of a reference crystal structure of a component at different nominal pixel sizes. Currently we do this manually, using `fitmap` in UCSF Chimera, but given the sophisticated set of tools in Phenix for fitting atomic models and analyzing real space correlations, I was wondering if a tool in Phenix already exists to do this, or whether there would be any interest in adding such a tool at some point? Cheers Oli

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an atom moves away during model refinement
by Dmitry Semchonok 06 Nov '23

06 Nov '23

Dear colleagues, While refining my model, the Mg atom for some of the margin units moves far away from them. I am also using the ELBOW files of Mg during the refinement. What is the way to restrict the movement of atoms during refinement? I found that this behaviour can be observed after simulated annealing is on. And the harmonic_restraints may be acquired to restrict atom movement. Is that right? I am using the GUI version of Phenix, and I cannot see those parameters. Thank you. Sincerely, Dmitry

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phenix.real_space_diff_map - difference between output maps
by Jose Artur Brito 31 Oct '23

31 Oct '23

Dear All, I am trying to use phenix.real_space_diff_map to assess "reminiscent" density in a 1.9 A cryoEM map. Can someone explain the difference between map_model_difference_1.ccp4 and map_model_difference_2.ccp4 that PHENIX outputs? Thanks in advance, best, Jose --

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Re: [phenixbb] Pb LocalResolutionMap calculation
by CUNIASSE Philippe 31 Oct '23

31 Oct '23

Hi Tom, i dowloaded and installed the nightly builds 1.21rc1-5134 but i do not see a direct access to the n_boxes parameter in the gui of the local Resolution Map menu. Is that normal, is it in the previous nightly build (5133)? Another question : in the gui of the local Resolution Map menu, i can see the value of the parameters by navigating the parameters menu, but i cannot modified their values. Is that normal an how to solve it ? Thank you so much for your help. Best regards. Philippe. ________________________________ De : phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> de la part de CUNIASSE Philippe Envoyé : dimanche 29 octobre 2023 22:06:55 À : Tom Terwilliger Cc : phenixbb(a)phenix-online.org Objet : [PROVENANCE INTERNET] Re: [phenixbb] Pb LocalResolutionMap calculation Hi Tom, Thank you so much. I will test some values of this n_boxes parameter. Best regards. Philippe. ________________________________ De : Tom Terwilliger <tterwilliger(a)newmexicoconsortium.org> Envoyé : dimanche 29 octobre 2023 14:03:45 À : CUNIASSE Philippe Cc : phenixbb(a)phenix-online.org; Tom Terwilliger Objet : Re: [phenixbb] Pb LocalResolutionMap calculation Hi Philippe, Yes, certainly the number of boxes affects the resulting local_resolution map. The 2400 boxes correspond to 14x14x14 boxes for a cubic map which means that you have only a gradual sampling along any axis of your map. You can adjust the number of boxes with the parameter n_boxes=2400. In the GUI, search under "All parameters" for "box" and you'll get the entry form. I will move this to the front page in tomorrow's nightly build of Phenix so it is easier to set. All the best, Tom T On Sun, Oct 29, 2023 at 3:42 AM CUNIASSE Philippe <Philippe.CUNIASSE(a)cea.fr<mailto:[email protected]>> wrote: Hi Tom, thank so much you for your answer. I uploaded the nigthtly build and it worked far better (a couple of hours) and ended correctly. I noticed that the gain was due to the fact the only about 2400 boxes were calculated (in place of more than 40000 in my slow previous calculation, likely explaining the gain of a factor 20). As i have a very large map, i wonder how this affects the quality of the LocalResolutionMap. And i also wonder if there is a mean to define this parameter to study this effect. Thank you so much for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ ----------------------------------------------- ________________________________ De : Tom Terwilliger <tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]>> Envoyé : vendredi 27 octobre 2023 11:04:52 À : CUNIASSE Philippe Cc : phenixbb(a)phenix-online.org<mailto:[email protected]>; Tom Terwilliger Objet : Re: [phenixbb] Pb LocalResolutionMap calculation Hi Philippe, I'm sorry for the slow calculation...the problem is the number of boxes is too high. If you download a nightly build like this one: https://phenix-online.org/download/phenix/nightly/?version=1.21rc1-5130 then it should be a lot faster (still not quick, but in your case should be 20x faster). All the best, Tom T On Fri, Oct 27, 2023 at 2:16 AM CUNIASSE Philippe <Philippe.CUNIASSE(a)cea.fr<mailto:[email protected]>> wrote: Dear all, i try to calculate local resolution maps with phenix since a couple of days. It turns out that the calculation seems very slow and i suspect that there is a problem because i even cannot stop the calculation with the abort button in the gui. In my last run (still running), i use 2 half-maps and the program can read them correctly, start the calculation by returning that 42875 boxes are considered. I run it on my MacBook pro (M1 running OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs. However, with this calculation (and also a smaller map with about 17000 boxes on 1CPU), the calculations run more than 24 hours without finishing. I wonder if there coud be a problem and if no, what could be the duration of such calculation. Thanks in advance for your help. Best regards. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2661676233] ----------------------------------------------- _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org<mailto:[email protected]> http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org<mailto:[email protected]> -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]> Tel: 505-431-0010 -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org<mailto:[email protected]> Tel: 505-431-0010

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Pb LocalResolutionMap calculation
by CUNIASSE Philippe 29 Oct '23

29 Oct '23

Dear all, i try to calculate local resolution maps with phenix since a couple of days. It turns out that the calculation seems very slow and i suspect that there is a problem because i even cannot stop the calculation with the abort button in the gui. In my last run (still running), i use 2 half-maps and the program can read them correctly, start the calculation by returning that 42875 boxes are considered. I run it on my MacBook pro (M1 running OSX 13.4 with 32Gb RAM) on 4 cpu. The calculation actually runs on 4 CPUs. However, with this calculation (and also a smaller map with about 17000 boxes on 1CPU), the calculations run more than 24 hours without finishing. I wonder if there coud be a problem and if no, what could be the duration of such calculation. Thanks in advance for your help. Best regards. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2661676233] -----------------------------------------------

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an installation issue
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear colleagues, Installing phenix of WSL I received an error - david@DESKTOP-NMD1JP9:~$ phenix [1] 402 david@DESKTOP-NMD1JP9:~$ Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/Error.py", line 76, 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 "/usr/local/phenix-1.21rc1-5130/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21rc1-5130/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21rc1-5130/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21rc1-5130/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) 1. it is a new Desktop and WSL; 2. Additionally, I installed python 3. I run sudo locale-gen "en_GB.UTF-8" (but maybe there is a command to check if it works properly) 4. on my laptop WSL phenix works nicely Any advice? Many thanks. Sincerely, Dmitry

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Apply NFC operators to helical structure
by Dmitry Semchonok 22 Oct '23

22 Oct '23

Dear colleagues, Please prompt me on correctly applying the symmetry parameters to the helical cryo-em map. What I did: 1. Found symmetry with Map symmetry. The process finished successfully. 2. Applied the NFC operators. But the outcome has only two units (C2 symmetry). When I put more units in the program setting, nothing happens after the run; moreover, the output is not generated. Could you please advise how to fill the helical cryo-EM structure with units? Many thanks for considering my request. Sincerely, Dmitry

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convergence in Phenix real space refinement
by Robert Oeffner 20 Oct '23

20 Oct '23

Hi, I'm curious to know when convergence has been obtained in phenix_real_space_refine. I see the number "moved from start" in the log file and assume that once it doesn't change much after several macro cycles then convergence has been obtained when refining a structure. True? What is that value based on, the RMSD between the initial structure and the final structure? I didn't find this documented in the 2018 publication of the program. Many thanks, Rob

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Renumbering while retaining refinement info
by Patrick Loll 15 Oct '23

15 Oct '23

Hello all, I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I’m working with a truncated construct (like a dope I didn’t do this at the outset). However, when I run PDB Tools, it does not write the refinement information into the output CIF. Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not so much in mmCIF). Cheers, Pat __________________________________ Patrick J. Loll, PhD (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St. Philadelphia, PA 19102-1192 USA (267) 359-2653 pjl28(a)drexel.edu

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