- phenixbb - phenix-online.org

More stringent water picking
by Schubert, Carsten [PRDUS] 19 Mar '07

19 Mar '07

Hi, is it possible to increase the stringency criteria for picked waters, besides increasing the sigma level? E.G. something on the order of the H-bonding criterion found in CNS? I find that the automated water-picking routine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps. Thanks Carsten

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Re: [phenixbb] More stringent water picking
by Schubert, Carsten [PRDUS] 19 Mar '07

19 Mar '07

Thanks Guys, would it be possible to implement the H-bonding criteria? From my experience with CNS it worked quite nicely. Right now I end up with ~350 waters in a 2.3 A structure of a 30kDa protein, which is a bit much. -----Original Message----- From: phenixbb-bounces(a)phenix-online.org [mailto:[email protected]] Sent: Monday, March 19, 2007 1:02 PM To: PHENIX user mailing list Subject: Re: [phenixbb] More stringent water picking Hi Carsten, thanks for your question! The main water picking criteria in phenix.refine are: 1) Fo-Fc map; 2) 2Fo-Fc map; 3) macromolecule - water distance; 4) water-water distance; 5) B-factors and occupancies max/min values; plus some more of expert level ... There is no specific H-bonding criteria implemented. You can play with sigma cutoff for both maps and with the distances above. In most of the cases it the reasonable behavior. I would be interested in Paul's (Adams) comments about his experience of usefulness of H-bonding criteria in CNS. Thanks! Pavel. Schubert, Carsten [PRDUS] wrote: Hi, is it possible to increase the stringency criteria for picked waters, besides increasing the sigma level? E.G. something on the order of the H-bonding criterion found in CNS? I find that the automated water-picking routine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps. Thanks Carsten _____ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org <mailto:[email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb <http://www.phenix-online.org/mailman/listinfo/phenixbb>

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Re: [phenixbb] OS X installation problem
by Ralf W. Grosse-Kunstleve 17 Mar '07

17 Mar '07

> powerpc-apple-darwin8-g++-4.0.0 (GCC) 4.0.0 20041026 (Apple Computer, > Inc. build 4061) There is a more recent Xcode release that works here. I.e. if you still want to compile from sources, upgrade the Xcode tools. You can get them for free at Apple's developer web site. However... > is that the 10.3.9 bundle? Yes, exactly. I should also work under 10.4. I recommend trying this first. It is also most faster than a source installation (just a few seconds). Ralf

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Re: [phenixbb] OS X installation problem
by Ralf W. Grosse-Kunstleve 17 Mar '07

17 Mar '07

I have not seen this error before. Could you send me the output of c++ --version Note that we have binary bundles for PowerPC Macs. Did you try that one? Ralf

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OS X installation problem
by Arthur Glasfeld 17 Mar '07

17 Mar '07

Hi, I'm following Bill Scott's instructions for installing cci_apps on a G5 mac. I've attempted it from the self-extracting file and from the gzipped file. I type the following commands: /System/Library/Frameworks/Python.framework/Versions/Current/bin/ python ../cci_apps_sources/libtbx/configure.py phenix source setpaths.sh num_cpu=$( sysctl hw.logicalcpu | awk '{print $NF}' ) libtbx.scons -j $num_cpu . and things begin OK, but then after a bit of compiling, I get: /usr/local/cci_apps/cci_apps_sources/boost/libs/python/src/object/ inheritance.cpp:120: instantiated from here /usr/local/cci_apps/cci_apps_sources/boost/boost/graph/ graph_concepts.hpp:74: error: base 'boost::concepts::IncidenceGraph<boost::reverse_graph<boost::<unnamed>:: cast_graph, const boost::<unnamed>::cast_graph&> >' with only non- default constructor in class without a constructor scons: *** [boost/libs/python/src/object/inheritance.o] Error 1 scons: building terminated because of errors. usr+sys time: 5.92 seconds wall clock time: 37.99 seconds I had no problems in an intel mac. Anything obvious I should have done? Thanks in advance for any assistance, Arthur Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA

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Re: [phenixbb] phenix.refine crash -- other error
by Peter Zwart 16 Mar '07

16 Mar '07

Good to know. Let me know if the refinement is any faster. Cheers Peter Ulrich Baumann wrote: > Yop, that did it --- I sourced an old phenix setpaths and not the cci_apps. > > Thanks a lot, > > Ulrich > > Quoting Peter Zwart <PHZwart(a)lbl.gov>: > >> Hi Ulrich, >> >> Please make sure that the phenix.python used is actually the >> phenix.python you installed with cci_apps. >> >> The behavoir seen might be due to using an other phenix.python >> installation (on that loads in old python libraries). This can be >> avoided by making sure that the last crystallographic package sourced in >> your .chsrc file, is the latest phenix/cci_apps installation. >> >> A which phenix.python might give a clue what is run, and hitting the tab >> key or CRTl-D after typing phenix.refine might auytocomplete or give a >> list of possibilities. >> >> Let me know what happened. >> >> >> Peter >> >> >> >> >> >> >> >> >> >> Ulrich Baumann wrote: >>> Hi Peter, >>> >>> I hate to bother you guys with this but .... >>> >>> dcb-macbeth:[lip3] > phenix.python >>> /usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py >>> data.file=lip_r3_1.8A.mtz model.file=in.pdb action=reindex >> standard_laws=niggli >>> #phil __OFF__ >>> ================= >>> REINDEX >>> A reindexing tool >>> ================= >>> >>> Traceback (most recent call last): >>> File >> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py", >>> line 468, in ? >>> reindex_utils(sys.argv[1:]) >>> File >> "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/examples/reindex.py", >>> line 260, in reindex_utils >>> combined_xs = crystal.select_crystal_symmetry( >>> AttributeError: 'module' object has no attribute 'select_crystal_symmetry' >>> >>> >>> I seem to hae to set a spacegroup? Sorry, I could not find a documentation >> for >>> the reindex utility. >>> >>> Many thanks, >>> >>> Ulrich >>> >>> Quoting Peter Zwart <PHZwart(a)lbl.gov>: >>> >>>> Hi Ulrich, >>>> >>>> You could try refining your structure in a primitive setting, this might >>>> alleviate memory usage a bit (not sure though). >>>> >>>> try >>>> >>>> phenix.python $MMTBX_DIST/mmtbx/examples/reindex.py data.file=mydata.mtz >>>> model.file=mymodel.pdb action=reindex standard_laws=niggli >>>> >>>> You will get a new mtz file and a new pdb file. Unfortunately, the free >>>> flags are not copied over, so you would have to reindex those separately >>>> using iotbx.reflection_file_converter and read that file in separately >>>> in phenix.refine. >>>> >>>> This might be a bit criptic, if so, let me know and I will post more >>>> details. >>>> >>>> I am not sure this does the trick though, I hope Ralf or Pavel can give >>>> some suggestions. >>>> >>>> Cheers >>>> >>>> Peter >>>> >>>> >>>> >>>> >>>> Ulrich Baumann wrote: >>>>> Hi there, >>>>> >>>>> if you remove the ANISOU card from the input pdb file, phenix will run >>>> fine >>>>> ....sometimes not. >>>>> >>>>> phenix.refine ( Version: 2007_01_24_2154) crashed for me as well: we >> have >>>> a >>>>> rather large unit cell and good resolution. The program crashes >>>> reproducibly >>>>> (see below) when using resolution limits better than 3 A, although >>>> sometimes >>>>> this only occurs in the 2nd macrocycle. >>>>> >>>>> Working crystal symmetry after inspecting all inputs: >>>>> Unit cell: (202.401, 202.401, 317.731, 90, 90, 120) >>>>> Space group: R 3 :H (No. 146) >>>>> >>>>> >>>>> We have 2 GB memory and could stuff in more but maybe we can limit the >>>> memeory >>>>> use in a different way? >>>>> >>>>> >>>>> Thanks a lot for your help, >>>>> >>>>> Ulrich >>>>> >>>>> >>>>> ============================= ml refinement start >>>> ============================= >>>>> ----------structure factors based statistics (before >>>> refinement)---------- >>>>> Traceback (most recent call last): >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.p >>>>> y", line 5, in <module> >>>>> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/command_li >>>>> ne.py", line 75, in run >>>>> call_back_after_monitor_collect=call_back_after_monitor_collect) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/driver.py" >>>>> , line 1108, in run >>>>> log = log) >>>>> File >>>> "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/refinement/strategies >>>>> .py", line 174, in refinement_machine >>>>> abcd = abcd) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", >> line >>>> 185, >>>>> in __init__ >>>>> b_cart = b_cart) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/f_model.py", >> line >>>> 466, >>>>> in update_xray_structure >>>>> f_mask = bulk_solvent_mask_obj.structure_factors(miller_set= >>>> self.f_obs) >>>>> File "/usr/local/cci_apps/cci_apps_sources/mmtbx/mmtbx/masks.py", line >>>> 97, in >>>>> structure_factors >>>>> flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real())) >>>>> MemoryError >>>>> >>>>> ---------------------------------------------------------- >>>>> ------------------------------------------------------- >>>>> Quoting Pavel Afonine <pafonine(a)lbl.gov>: >>>>> >>>>>> Hi, >>>>>> >>>>>> this is known problem and it will be fixed ASAP; sorry for this. >>>>>> This presumably happens because an atom selected to be refined as >>>>>> individual anisotropic is included into a TLS group. >>>>>> I will let you know once the fixed version of CCI Apps is available. >>>>>> >>>>>> Pavel. >>>>>> >>>>>> >>>>>> >>>>>> Jianghai Zhu wrote: >>>>>>> Hi, >>>>>>> >>>>>>> I was using phenix.refine from the latest cci apps bundle to do >>>>>>> tls+individual_sites+individual_adp refinement. The program crashed >>>>>>> with the following error message. >>>>>>> >>>>>>> ----------Target weights (before refinement)---------- >>>>>>> >>>>>>> >>>>>>> Traceback (most recent call last): >>>>>>> File >>>>>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py", >>>>>>> line 5, in <module> >>>>>>> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py", >>>>>>> line 75, in run >>>>>>> call_back_after_monitor_collect=call_back_after_monitor_collect) >>>>>>> File >>>>>>> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py", >>>>>>> line 1108, in run >>>>>>> log = log) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py", >>>>>>> line 245, in refinement_machine >>>>>>> log = log) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py", >>>>>>> line 222, in __init__ >>>>>>> compute_gradients = True) >>>>>>> File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", >>>>>>> line 144, in energies_adp_aniso >>>>>>> xray_structure = xray_structure, >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", >>>>>>> line 109, in __init__ >>>>>>> self.check_flags(fl_i) >>>>>>> File >>>>>>> >> "/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py", >>>>>>> line 177, in check_flags >>>>>>> assert not fl.use_u_aniso() >>>>>>> AssertionError >>>>>>> >>>>>>> Anyone has any idea what is happening? Thanks. >>>>>>> >>>>>>> Jianghai >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++ >>>>>>> Jianghai Zhu, Ph.D >>>>>>> CBR Institute for Biomedical Research >>>>>>> Department of Pathology >>>>>>> Harvard Medical School >>>>>>> 200 Longwood Ave., Boston, MA 02115 >>>>>>> Ph: 617-278-3211 >>>>>>> Fx: 618-278-3232 >>>>>>> +++++++++++++++++++++++++++++++ >>>>>>> >>>>>>> >>>>>>> >>>>>>> >> ------------------------------------------------------------------------ >>>>>>> _______________________________________________ >>>>>>> phenixbb mailing list >>>>>>> phenixbb(a)phenix-online.org >>>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>>>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> phenixbb(a)phenix-online.org >>>> http://www.phenix-online.org/mailman/listinfo/phenixbb >>>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >> > >

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Re: [phenixbb] pdb waters
by Pavel Afonine 16 Mar '07

16 Mar '07

Hi, yes, the waters in your file do not match the Monomer Library definition. If you simply replace O1 with O that will fix the problem. For example: GOOD record: ATOM 22792 O HOH X 1 37.309 34.504 -14.174 1.00 38.28 O BAD record: ATOM 22792 O1 HOH X 1 37.309 34.504 -14.174 1.00 38.28 O > I have tried running elbow on my pdb already with no luck. using your > command I get the error message: elbow.builder: error: no such option: > --do-all That makes me thinking that you are using an old version of CCI Apps or PHENIX. Are you using the latest one? Is the command you run looks like: % elbow.builder x.pdb --do-all Nigel: do you have any comments? Pavel.

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Re: [phenixbb] Few questions -- FreeR flag specification
by Tom Terwilliger 15 Mar '07

15 Mar '07

Hi John, I'm sorry for the slow reply; I was on a site visit and out of email contact. The AutoBuild wizard in the current version (which I am afraid you probably do not have!) does try to take the FreeR flags from your input file. You can also tell it specifically to do so with the GUI and in the command-line with refinement_file=ref.mtz input_refinement_labels="FP SIGFP None None None None None None FreeR" If you have version 1.25a , then you still should be able to specify the column for FreeR flags in the GUI window that asks which column labels to use (I could be wrong about that, however, as I don't have this version on my computer any longer). You should also be able to specify them with a script: phenix.runWizard AutoBuild AutoBuild.start_from_model terwill@rosie> cat $PHENIX/phenix/phenix/wizard_scripts/AutoBuild.start_from_model # AutoBuild.start_from_model # script to run a AutoBuild starting from a model # Version 1.26 of 26-Jan-2007 # run with: # phenix.runWizard AutoBuild AutoBuild.start_from_model [restart] # if you specify restart it will forget everything, # otherwise it will continue on from where it is now. input_ncs_file NONE # heavy-atom or PDB file for finding NCS input_data_file $PHENIX/examples/p9-sad/solve_1.mtz # file with experimental data. # Can be any format if only FP SIGFP; must be mtz if phases or HL or FreeR input input_labels FP SIGFP None None None None None None FreeR_flag # optional # line defining the 9 columns in input_mtz_file corresponding to # FP SIGFP PHIB FOM HLA HLB HLC HLD FreeR (use "None" for missing) input_map_file $PHENIX/examples/p9-sad/resolve_1.mtz # Optional map-coefficients file for first rebuild input_map_labels FP PHIM FOMM # optional line defining the 3 columns # in input_map_file corresponding to FP PHIB FOM ("None" for missing) input_seq_file $PHENIX/examples/p9-sad/seq.dat # file with sequence in 1-letter form # separate chains with >>> resolution 2.5 # high-resolution limit solvent_fraction 0.60 # you can put any other parameters here input_pdb_file $PHENIX/examples/p9-sad/p9.pdb # input PDB file for rebuilding rebuild_in_place True # rebuild my_model.pdb in place # (as opposed to building from scratch) start_chains_list 4 # chain 1 starts at residue 4 # rebuild residues 21-27 of chain "" and 31-42 of chain "" # rebuild_res_start_list 21 31 # rebuild_res_end_list 27 42 # rebuild_chain_list "" "" # n_cycle_rebuild_min 5 # n_cycle_rebuild_max 10 # AutoBuild will run automatically from here on with no more inputs I hope that helps! The new version of PHENIX that will be out very soon fixes many other problems as well! All the best, Tom T At 03:26 AM 3/13/2007, john kryst wrote: >Hi phenixbb !! > > I have few questions. > >1. Is there any utility in phenix to write out pdb formatted (which >is ready to deposit) output file.. like xtal_pdbsubmission utility in CNS. >2. In Autobuild wizard how to ask the program to use the Free R >flags present in the file. It always generates new Free R flags >during refinement. >One general question. > >Does the rmsd estimation (for eg. rmsd_bonds ) depends on the >program we use ?? > >I have been refining in CNS. then i used Autobuild wizard to build >my model. when i went back to cns the rmsd of bond increased ( >0.0218 A). But phenix.refine says it it 0.007A. > >Thanks in advance for your kind inputs. > >regards >john >_______________________________________________ >phenixbb mailing list >phenixbb(a)phenix-online.org >http://www.phenix-online.org/mailman/listinfo/phenixbb Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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Re: [phenixbb] phenix.refine problems with my pdb
by Nicholas Noinaj 15 Mar '07

15 Mar '07

matt, can't offer much help, but have you tried to remove the ligand and try refinement? it would let you know if the pdb file or the presence of the ligand is the problem. at least let you would know where you should focus your attention. if all else fails, have you tried getting parameters for your ligand from the PRODRG Server and using that for inputing the ligand parameters into phenix.refine directly when you setup the refinement job? (I think i have done this before???) here is the website in case you aren't familiar... http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ Again, Best of luck! cheers, nick -----Original Message----- From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> To: phenixbb(a)phenix-online.org Date: Thu, 15 Mar 2007 13:00:42 +0000 Subject: [phenixbb] phenix.refine problems with my pdb Dear All, I am trying to run phenix.refine but I keep getting the message: Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 308 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions. Note that elbow.builder is available to create restraint definitions. I have run my ligands through elbow and used the output .cif but I still get the same message. I can find no info on this problem in the manual or the BB, can anyone help? Thanks in advance, yours, Matt. Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825 _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Re: [phenixbb] phenix.refine problems with my pdb
by Nicholas Noinaj 15 Mar '07

15 Mar '07

matt, >>> Number of atoms with unknown nonbonded energy type symbols: 308 just curious, did you have 308 waters? as peter said, hard to determine exact problem without some files or examples to look at. also phenix does a good job with water picking, in my little experience. just one more question, when you do get the refinement to work, is your ligand(s) included with the protein model? just no waters, right? it wasn't completely clear from your message. if the ligands aren't included, i recommend adding it(them) back and see if refinement works. then if that works, try water picking within phenix. again, best of luck. cheers, nick -----Original Message----- From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> To: noinaj(a)uky.edu, PHENIX user mailing list <phenixbb(a)phenix-online.org> Date: Thu, 15 Mar 2007 14:15:45 +0000 Subject: Re: [phenixbb] phenix.refine problems with my pdb Thanks for replies so far.... I removed all ligands and then waters - the waters seem to be the problem as the protein model is now refining, do they need to be treated/marked in a different way for phenix? Thanks again, Matt. On 15 Mar 2007, at 13:32, Nicholas Noinaj wrote: > matt, > > can't offer much help, but have you tried to remove the ligand and > try refinement? it would let you know if the pdb file or the > presence of the ligand is the problem. at least let you would know > where you should focus your attention. > > if all else fails, have you tried getting parameters for your > ligand from the PRODRG Server and using that for inputing the > ligand parameters into phenix.refine directly when you setup the > refinement job? (I think i have done this before???) > > here is the website in case you aren't familiar... > http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ > > Again, Best of luck! > > > > cheers, > nick > > > -----Original Message----- > From: Matthew Bowler <mwb(a)mrc-dunn.cam.ac.uk> > To: phenixbb(a)phenix-online.org > Date: Thu, 15 Mar 2007 13:00:42 +0000 > Subject: [phenixbb] phenix.refine problems with my pdb > > Dear All, > I am trying to run phenix.refine but I keep getting the message: > > > Sorry: Fatal problems interpreting PDB file: > Number of atoms with unknown nonbonded energy type symbols: 308 > Please edit the PDB file to resolve the problems and/or supply a > CIF file with matching restraint definitions. Note that > elbow.builder is available to create restraint definitions. > > I have run my ligands through elbow and used the output .cif but I > still get the same message. I can find no info on this problem in > the manual or the BB, can anyone help? Thanks in advance, yours, > Matt. > > > > > > Matthew Bowler > MRC Dunn Human Nutrition Unit > Wellcome Trust / MRC Building > Hills Road > Cambridge CB2 2XY > Tel: 0044 (0) 1223 252826 > Fax: 0044 (0) 1223 252825 > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb Matthew Bowler MRC Dunn Human Nutrition Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 2XY Tel: 0044 (0) 1223 252826 Fax: 0044 (0) 1223 252825

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