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error loading SHELXL HKLF4 reflection file
by jonathan elegheert 22 Jun '09

22 Jun '09

Dear phenix developers, I am using the one of the latest phenix.refine nightly builds, and I'm trying to load a SHELXL .hkl file into phenix; phenix.refine xxx_refine_004.def xray_data.file_name="/path/xxx.hkl"=hklf4 The "Iobs,SigIobs"labels are well recognized (so the "Merging symmetry-equivalent intensities" subroutine works ok), but the necessary "=hklf4" or "=intensities" appendage seems to cause problems. The strange thing is that in phenix.xtriage, the same command line flag works perfectly fine. Thank you for any pointers! Jonathan Elegheert PhD student Ghent University -------------- Traceback (most recent call last): File "/usr/local/phenix-1.4-95/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-95/phenix/phenix/refinement/command_line.py", line 245, in __init__ log = self.log) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 201, in __init__ self.raw_flags = self.extract_flags(data = self.raw_data) File "/usr/local/phenix-1.4-95/cctbx_project/mmtbx/utils.py", line 266, in extract_flags parameter_scope = self.flags_parameter_scope) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 566, in get_r_free_flags miller_arrays = self.get_miller_arrays(file_name=file_name) File "/usr/local/phenix-1.4-95/cctbx_project/iotbx/reflection_file_utils.py", line 406, in get_miller_arrays if (os.path.samefile(canonical_file_name, tabulated_file_name)): File "/usr/local/phenix-1.4-95/build/intel-linux-2.6-x86_64/base/lib/python2.6/posixpath.py", line 153, in samefile s2 = os.stat(f2) OSError: [Errno 2] No such file or directory: '/path/xxx.hkl=hklf4'

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Re: [phenixbb] scaling
by Thomas C. Terwilliger 20 Jun '09

20 Jun '09

Hi, You can use autosol to do scaling of any pair of datasets, so if you just run the command below N times, once for each reference/to-be-scaled dataset pair you are interested in, it should do what you want: phenix.autosol native.data=native.sca deriv.data=deriv.sca correct_aniso=false skip_xtriage=true res_hyss=100 build=false this will stop with " HYSS failed...Probably no iso or ano differences.." because we are not giving HYSS any data. Then the file: AutoSol_run_1_/TEMP0/AutoSol_run_1_/TEMP0/mir_fbar.mtz will have the scaled native and deriv data in mtz format. For subsequent runs, the data will be in AutoSol_run_2_ ...etc I hope that helps! -Tom T >>> where ought i look for a phenx utility to scale any number of data sets >>> to >>> a reference data set? something akin to scale.inp in CNS. >> >> I don't think we have such a utility, unless there is something in >> solve (Tom?). -- But you shouldn't need this for any of the phenix >> applications. All trivial scaling of the scale.inp type is done >> on-the-fly. >> Ralf >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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scaling
by Bryan W. Lepore 19 Jun '09

19 Jun '09

where ought i look for a phenx utility to scale any number of data sets to a reference data set? something akin to scale.inp in CNS. -bryan

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Can I limit the model's B factor range during refinement
by junfeng liu 18 Jun '09

18 Jun '09

Dear all, Several models have been refined using Phenix recently. It works well . But the model's B factors in some region are very high, higher than 150 or more. Of course, the wilson B is high too, about 60-70. I remembered that the B factor can be limited in the refinement using Refmac. Can I do the similar thing in Phenix ? Thanks in advance! Best wishes, leo

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Molecular replacement
by Colin Levy 17 Jun '09

17 Jun '09

Within Phenix, is it possible to specify and lock the centre of rotation for a molecular replacement search. I have a single intrinsic anomalous scatterer within my protein which I can locate easily, therefore I would like to manually specify this point as the centre of rotation and then carry out a rotation search only about this single fixed point. Thanks for any suggestions, Colin

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Re: [phenixbb] Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Thanks a lot Nigel, I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way. Thanks again in advace. YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand YoungJin If you opened the CIF in REEL you can right-click on the P-N bond and change the order to single. You can then use the menu Action -> Build -> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen. Nigel On 6/16/09 9:03 AM, Young-Jin Cho wrote: Thanks Nigel, I opened ANP and truncated the terminal PO3 and ran phenix.ready_set. When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine. So if you can tell me how I can handle to put correct geometry, it will be great. Cheers, YoungJin ----- Original Message ----- From: "Nigel W Moriarty" <NWMoriarty(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand Young-Jin You need to check that you and the PDB ligand database are talking about the same thing. You can see what the ligand ANP is by phenix.reel --chemical-components=ANP If you have the non-hydrogen atoms of your truncated ligand, phenix.ready_set will add the hydrogens and may even add the correct number of hydrogens to the terminal nitrogen. But what about its name? I would recommend find the three-letter code that corresponds to your ligand. Nigel On 6/15/09 7:01 PM, Young-Jin Cho wrote: Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat! _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://www.phenix-online.org/mailman/listinfo/phenixbb

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Adding H atoms onto ligand
by Young-Jin Cho 16 Jun '09

16 Jun '09

Let me excuse to post another similar issue. I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb. As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's. I did Molprobity as in the general case to add H atoms, but it didn't make it. Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below: Processing inputs. This may take a minute or two. Sorry: Ambiguous parameter definition: remove = element H Best matches: refinement.refine.occupancies.remove_selection refinement.geometry_restraints.remove.angles refinement.geometry_restraints.remove.dihedrals refinement.geometry_restraints.remove.chiralities refinement.geometry_restraints.remove.planarities Thanks in advance, YoungJin ps. Tanks Nat!

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specification of column labels in command line promt
by Raja Dey 15 Jun '09

15 Jun '09

Dear Friend, I was trying to analyse one of my data set. I am getting the following error. Multiple equally suitable arrays of observed xray data found. Possible choices: Cam-pk-hr_scala1.mtz:IMEAN_pk,SIGIMEAN_pk Cam-pk-hr_scala1.mtz:I_pk(+),SIGI_pk(+),I_pk(-),SIGI_pk(-),merged Please use scaling.input.xray_data.obs_labels to specify an unambiguous substring of the target label. Sorry: Multiple equally suitable arrays of observed xray data found. I have the following column labels in my .mtz file * Column Labels : H K L FreeR_flag F_pk SIGF_pk F_pk(+) SIGF_pk(+) F_pk(-) SIGF_pk(-) DANO_pk SIGDANO_pk IMEAN_pk SIGIMEAN_pk I_pk(+) SIGI_pk(+) I_pk(-) SIGI_pk(-) How I can specify column labels in a command line promt? Say, I want to use IMEAN_pk & SIGIMEAN_pk Thanks... Raja

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phenix and PAE kernels
by nick＠silvaggi.com 15 Jun '09

15 Jun '09

Dear List, Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels? I have looked on phenix-online.org, but did not find anything. This problem is independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3, and several releases of cci_apps) and occurs with almost all of the programs (most fail in the cci_apps test_apps script). The problem appears to be specific to the PAE kernels, since the same programs run fine in the non-PAE counterparts. I am running Fedora 10 with kernel versions 2.6.27.24-170.2.68/PAE and 2.6.27.21-170.2.56/PAE. Phenix programs fail under both PAE kernels, but are fine under the non-PAE kernels. Thanks in advance for any help you can provide. Best regards, Nick Silvaggi long int too large to convert Traceback (most recent call last): File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/builder.py", line 10, in <module> from elbow.chemistry.any_chemical_format_reader \ File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/any_chemical_format_reader.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 16, in <module> File "/usr/swr/cci_apps/cci_apps_sources/elbow/elbow/utilities/monomer_utilities.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 4, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 3, in <module> File "/usr/swr/cci_apps/cci_apps_sources/mmtbx/mmtbx/refinement/print_statistics.py", line 2, in <module> File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 1, in <module> # packaging File "/usr/swr/cci_apps-07_25_1259/cci_apps_sources/elbow/elbow/command_line/__init__.py", line 518, in <module> File "/usr/swr/cci_apps/cci_apps_sources/boost_adaptbx/boost/python.py", line 68, in __init__ OverflowError: long int too large to convert

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phenix refine
by sbiswas2＠ncsu.edu 12 Jun '09

12 Jun '09

Hi all, I tried running phenix refine with a pdb file refined in cns. This has a glycerol molecule in it. I got the following message: Number of atoms with unknown nonbonded energy type symbols: 42 "ATOM 6921 OAA GLC J 1 .*.J " "ATOM 6922 CAD GLC J 1 .*.J " "ATOM 6923 CAF GLC J 1 .*.J " "ATOM 6924 OAC GLC J 1 .*.J " "ATOM 6925 CAE GLC J 1 .*.J " "ATOM 6926 OAB GLC J 1 .*.J " "ATOM 6927 OAA GLC J 2 .*.J " "ATOM 6928 CAD GLC J 2 .*.J " "ATOM 6929 CAF GLC J 2 .*.J " "ATOM 6930 OAC GLC J 2 .*.J " ... (remaining 32 not shown) Time building chain proxies: 11.79, per 1000 atoms: 1.69 Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown scattering type symbols: 42 Number of atoms with unknown nonbonded energy type symbols: 42 Does anyone know how to resolve this thanks, Shya

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