- phenixbb - phenix-online.org

Phenix autosol error 2L MAD
by Graeme Winter 10 Jul '12

10 Jul '12

Hi Folks, 2L MAD data set where SHELXC/D/E works fine I (repeatedly) get this error, through GUI or scripts... resolution: 1.7 recommended_resolution: 1.9 datafile_for_hyss: /Users/graeme/projects/test/12287_build/AutoSol_run_10_/TEMP0/ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca aniso_corrected: True aniso_b_min: 13.2 aniso_range_of_b: 6.8 RUNNING HYSS on ANISO_subset_PHX_I(+)_WAVE1.sca_ano_1.sca from PDS as miller arrays *************ERROR ENDING ******************* ******************************************************************************** Failed to carry out AutoSol_hyss: HYSS failed...Probably no iso or ano differences... ******************************************************************************** *************ERROR ENDING ******************* The data set works fine with a third (radiation damaged) data set. There is also a massive anomalous signal in the data (2L) as it stands. here's the PHIL: autosol { seq_file = 12287.seq sites = 8 atom_type = Se crystal_info { unit_cell = 51.59 51.59 157.69 90 90 90 space_group = "P 43 21 2" solvent_fraction = 0.52 chain_type = PROTEIN resolution = 0 change_sg = True } wavelength { data = subset.mtz lambda = 0.97966 f_prime = -9.9 f_double_prime = 3.9 labels = 'I(+)_WAVE1 SIGI(+)_WAVE1 I(-)_WAVE1 SIGI(-)_WAVE1' } wavelength { data = subset.mtz lambda = 1.00000 f_prime = -3.3 f_double_prime = 0.5 labels = 'I(+)_WAVE2 SIGI(+)_WAVE2 I(-)_WAVE2 SIGI(-)_WAVE2' } } Have I done something wrong? Thanks, Graeme

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special position
by Karolina Michalska 10 Jul '12

10 Jul '12

Hi all, I'm refining a structure with a phosphate ion on a 3-fold axis. I set occupancy manually to 0.33 and after refinement the ion has huge B-factor (close to 100) and there is a lot of positive electron density. I found somewhere that phenix recognizes special positions and there is not need to adjust occupancy manually. so I set it to 1 again and re-refined. This time my phosphate sits in a mixture of negative and positive density with B factor around 90 (for comparison Refmac refines it to ~20). Now I'm confused which procedure to follow. Karolina

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I/O error in writing very large B-factors
by Phil Jeffrey 09 Jul '12

09 Jul '12

This occurs at the end of refinement. Quite why it's trying to *read* from a string with Fortran-esque overflow formatting while in a writing step I don't know, but the PDB file gets truncated at REMARK IF THIS FILE IS FOR PDB DEPOSITION: REMOVE ALL FROM THIS LINE UP. The structure is not idyllic, clearly, but I'd like to see the extent of the problem rather than just the first atom. Got to be pretty easy to trap for and map to 999.99 either on the way in or out. Writing refined structure to PDB file: /Users/phil/Structures/reference_models/start_refine_001.pdb n_use = 21264 n_use_u_iso = 21264 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 21264 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 21264 Traceback (most recent call last): File "/usr/local/phenix-1.7.3-928/build/mac-intel-osx/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/command_line.py", line 105, in run refine_object.write_refined_pdb(f_pdb) File "/usr/local/phenix-1.7.3-928/phenix/phenix/refinement/driver.py", line 1379, in write_refined_pdb ignore_hd = not self.neutron_refinement) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 589, in __init__ ignore_hd = ignore_hd) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 504, in __init__ molprobity_scores=True) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model.py", line 1063, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__ self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 182, in analyze_clashes self.pdb_hierarchy = pdb.hierarchy.input(pdb_string=input_str).hierarchy File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/hierarchy.py", line 1044, in __init__ source_info=source_info, lines=flex.split_lines(pdb_string)) File "/usr/local/phenix-1.7.3-928/cctbx_project/iotbx/pdb/__init__.py", line 582, in input return ext.input(source_info=source_info, lines=lines) ValueError: string, line 5148: ATOM 17 N ILE A 268 -16.878 -22.262 49.415 1.00****** A N ------------------------------------------------------------^ not a floating-point number. Phil Jeffrey Princeton

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Iridium hexamine problems with eLBOW
by Benoît Masquida 07 Jul '12

07 Jul '12

I experience problems generating a correct CIF file for iridium hexamine (IRI in the eLBOW database). The geometry is supposed to be octahedral and eLBOW outputs a prism regardless of the options checked in the GUI. eLBOW actually does the same for the octahedral Mg(OH2)6. Does someone know how to rule this out? Thanks to everybody. Ben -- Benoît Masquida Chargé de Recherche CNRS IBMC Strasbourg UPR 9002 ARN b.masquida(a)ibmc-cnrs.unistra.fr +33 (0)3 88 41 70 45 +33 (0)6 70 23 79 50 +33(0)3 88 60 22 18 (fax)

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Subject: no kidding - we need small crystals!
by jens j birktoft 05 Jul '12

05 Jul '12

Hi everybody, Any suggestions regarding how to generate small!! crystals? Yes, in this case that is what we want While we can generate crystals of size 100-500 microns, this time we something in the range of .5-5 microns. Any ideas and suggestions would be greatly appreciated, Cheers Jens

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ask refinement question including an aligo as the ligand
by crystallogrphy 05 Jul '12

05 Jul '12

Hi, I want to refine my structure including a sugar oligomer as the ligand in Phenix GUI. I first put each subunit into the density and merge them together as the oligomer in Coot. Then I merged the oligomer coordinates to the protein file. Then I run phenix.elbow to get the cif file. Finally, I run phenix.refine. However, the oligomer units were pushed away from each other. I guess I need to modify the cif file to link the oligo units together. Does anyone know how I can I do it? thanks!

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Re: [phenixbb] phenixbb Digest, Vol 80, Issue 1
by Matthew J. Whitley 05 Jul '12

05 Jul '12

Hello, One simple thing that might be the problem: As I'm sure you know, oligosaccharides are formed via intermolecular dehydration reactions. If I understand you correctly, you built the oligosaccharide by loading the component monomers into the density in Coot and then joined them together. Whenever two sugars are joined together, three atoms are given off as a water molecule. Did you actually delete the appropriate oxygen and two hydrogens from your coordinates for each glycosidic linkage in your structure? If you didn't, then it doesn't matter whether you told Coot or Phenix that the monomers or linked, you'll still have atoms trying to occupy the same space and thus the refinement will blow them apart. Not that I have EVER made that mistake myself . . . Similar topics have come up on the Phenix BB before. For other possibly useful information, see: http://phenix-online.org/pipermail/phenixbb/2012-April/018390.html http://www.phenix-online.org/pipermail/phenixbb/2009-October/013951.html Good luck! Matthew --- Matthew J. Whitley, Ph.D. Postdoctoral Research Fellow Angela Gronenborn Lab Department of Structural Biology University of Pittsburgh School of Medicine On Wed, July 4, 2012 7:55 pm, phenixbb-request(a)phenix-online.org wrote: > > > Message: 14 > Date: Wed, 4 Jul 2012 15:28:09 -0400 > From: crystallogrphy <qunwan1(a)gmail.com> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: [phenixbb] ask refinement question including an aligo as the > ligand > Message-ID: > <CANcEHNi95ss+Tst8+8JVTK3=B598HjC_NNg5N7_=6-whdMTXpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I want to refine my structure including a sugar oligomer as the ligand in > Phenix GUI. > > I first put each subunit into the density and merge them together as the > oligomer in Coot. Then I merged the oligomer coordinates to the protein > file. Then I run phenix.elbow to get the cif file. Finally, I run > phenix.refine. However, the oligomer units were pushed away from each > other. I guess I need to modify the cif file to link the oligo units > together. Does anyone know how I can I do it? > > thanks!

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need subscription
by Afshan Begum 03 Jul '12

03 Jul '12

Dear Sir I have subscribe successfully to the phenixbb but i have not receive or involved in the discussion board could you kindly help ? Best Regards AFSHAN

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Question about mr-sad
by Edward A. Berry 02 Jul '12

02 Jul '12

in doing SAD phasing with the option: input_partpdb_file=MR.pdb Is it assumed MR.pdb is already located in the cell, or is it a model to be used in MR assisted by information from the heavy atom sites? Thanks, eab

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Re: [phenixbb] Default anisotropic B-factor refinement in phenix.refine?
by Filip YABUKARSKI 02 Jul '12

02 Jul '12

Hello again, First thank you very much for the response But in this case after the second run of phenix.refine i will lose the TLS contribution and the anisoU lines (?). How am I supposed to continue with TLS then (given it lowers my R factors i would be happy to keep it) and be sure that i do not refine anisotropic ADPs? Or you mean that i can do the 2 consecutive runs (with and without TLS) in the end of the refinement? Sorry if I got something wrong Filip On 2012-07-02 18:58, Pavel Afonine wrote: > Hi Filip, > > phenix.refine manual may need an update.. > > At 3A resolution if you run two consecutive refinements first with > TLS and the next one without TLS then in the second run anisotropic > ADPs will be converted to isotropic automatically. This is done by > phenix.refine to prevent accidental refinement of individual > anisotropic ADPs in such cases. The keyword and threshold are: > switch_to_isotropic_high_res_limit=1.5. > > Pavel > > On 7/2/12 9:47 AM, Filip YABUKARSKI wrote: >> Hello, >> >> I recently started to refine a structure with phenix.refine for a >> first time. It is a 3A dataset with NCS of 8. For the refinement i >> wanted to use TLS groups as well as individual B-factors >> (data/parameter ratio should be fine with ncs of 8) and after several >> cycles of refinement i get the Rfac of 20 and Rfree of 24 which is >> quite good (i also use simulated annealing, Secondary structure >> restraints and NCS restraints). Re-reading the refinement manual I >> realized that by using a PDB file which comes from a phenix.refine >> with TLS in the next refinement i am probably doing an anisotropic >> B-factor refinement for each atom, which in my case is not justified. >> I found a post on ccp4bb from 19 Fev 2009 discussing this issue but >> for me it is still not very clear. By reading the PDB i got from >> phenix.refine (version 1.7.3) it is not very clear (at least for me) >> if the refinement was with TLS groups and individual isotropic >> B-factors or with anisotropic B-factors. Basically my question is: if >> the input PDB has already anisoU records from a previous phenix.refine >> with TLS groups is the new phenix.refine going to use isotropic >> individual B-factors or anisotropic ones? (Even if in my case one can >> assume that i can probably use anisotropic B-factor refinement (24000 >> unique reflections with ncs of 8 vs. 6000 atoms in total) this is >> rarely the case for non-atomic resolution datasets) I would be very >> happy if someone gives an explanation. Many thanks >> >> Cheers >> Filip

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