- phenixbb - phenix-online.org

Re: [phenixbb] refinement with alternative molecules?
by Su-Chang Lin 28 Jan '10

28 Jan '10

Hi Ralf, I've done the refinement with alt. conf.. The occupancy is 0.58 for Mol A, 0.42 for Mol B. The maps look OK. R-factors drops a little bit. Before when I put Mol A in that region for refinement, I saw additional densities (a helix) for Mol B. When I put Mol B in the region for refinement, I saw additional densities (loops) for Mol A. Now with alt. conf. there are no additional densities. Can I use the occupancies for publication? Or do I need to do/check something else? Thanks! Su-Chang > Hi Su-Chang, > > I will try to refine the structure without NCS restraints. > I'd be interested to know how it goes, although I'm too busy to get > into the NCS code right now. > If the resolution is low I'd think it is better to use NCS, without > alt. conf. The mismatches you saw between related molcules may > be pure artifacts. But trying is better than guessing! > Ralf > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

3 2

new release of IL MILIONE
by Dritan Siliqi 28 Jan '10

28 Jan '10

1 0

Using LigandFit to identify unknown density
by Katya Heldwein 28 Jan '10

28 Jan '10

Hi, I'd like to run LigandFit to identify a small molecule accounting for an unknown density. How do I do that, preferably, in a command-line mode? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University School of Medicine 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

5 8

refinement with alternative molecules?
by Su-Chang Lin 27 Jan '10

27 Jan '10

Hi, Recently I got a crystal structure of a multiple-molecules protein complex. There are many protein subunits with the same fold. From the likelihood-weighted maps by Phenix, I can see two different subunits occupy the same position. (So I can put the model of either subunit in the same densities, but some loop regions and the C-terminal tail look different. ). I know Phenix can do occupancy refinement with a residue that has N alternative conformations. My question is can Phenix do occupancy refinement with alternative molecules? The RMSD for two subunits is about 1.3 angstrom. The sequence identity is about 30%. Thank you very much! Su-Chang Lin, Ph.D., Postdoc Associate Department of Biochemistry Weill Medical College, Cornell University Whitney Building, room W-212 1300 York Avenue, New York, NY 10021 212-746-6458

3 6

phenix.fmodel: a command line tool to compute structure factors from a model (Fcalc or Fmodel).
by Pavel Afonine 27 Jan '10

27 Jan '10

Starting PHENIX nightly build version 1.6-295 (2010-01-27), a new command line tool phenix.fmodel is available. This is a replacement for "phenix.pdbtools --f-model" command, which is not available anymore. phenix.fmodel is a comprehensive tool to compute structure factors from a model. For more information and usage examples simply run phenix.fmodel . Pavel. P.S. Below is the result of running phenix.fmodel: phenix.fmodel: a tool to compute structure factors, Fmodel: Fmodel = scale * exp(AnisoScale) * (Fcalc + k_sol * exp(-b_sol*s^2/4) * Fmask) where: - Fmodel - total model structure factor (complex value) - AnisoScale = -ht*A(-1)*b_cart*A(-1)th/4 - h - column vector with Miller indices - A - orthogonalization matrix - b_cart - anisotropic scale matrix - t and (-1) denotes transposition and inversion operations - scale - overall scale factor - Fcalc - structure factors calculated from atomic model - k_sol and b_sol - Flat Bulk solvent model parameters - Fmask - structure factors calculated from bulk solvent mask Usage examples: 1) phenix.fmodel model.pdb high_resolution=1.5 will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution. 2) phenix.fmodel model.pdb scale=2 k_sol=0.35 b_sol=50 b_cart="1 2 3 0 4 7" high_res=1.5 low_res=10 will result in a file containing complete set of Fmodel computed using the above formula in resolution range 1.5-20.0A. 3) phenix.fmodel model.pdb high_resolution=1.5 algorithm=direct is similar to "1)" but the Fcalc are computed using direct summation algorithm. 4) phenix.fmodel model.pdb high_res=1.5 format=cns label=FOBS type=real r_free=0.1 will result in CNS formatted file containing complete set of amplitudes of Fmodel = Fcalc computed up to 1.5A resolution, labelled as FOBS, and free-R flags with 10% of test reflections. This is a typical command to simulate Fobs. 5) phenix.fmodel model.pdb high_res=1.5 scattering_table=neutron will result in a file containing complete set of Fmodel = Fcalc computed from atomic model up to 1.5A resolution using neutron scattering table. 6) phenix.fmodel model.pdb parameters.txt will result in a structure factor file, where Fmodel were computed using parameters defined in parameters.txt file. The parameters.txt file can contain all or any subset of parameters listed below. Note, that each { must have a matching one }. 7) phenix.fmodel model.pdb reflection_data.mtz will result in a file containing a set of Fmodel = Fcalc that will match the set of Miller indices of the data in reflection_data.mtz file. 8) phenix.fmodel model.pdb reflection_data.mtz data_column_label="FOBS,SIGMA" similar to "7)", where the specific data array is selected. See below for complete list of available parameters. ------------------------------------------------------------------------------- Parameters to compute Fmodel:: high_resolution = None low_resolution = None r_free_flags_fraction = None add_sigmas = False scattering_table = wk1995 it1992 *n_gaussian neutron data_column_label = None fmodel { k_sol = 0.0 b_sol = 0.0 b_cart = 0 0 0 0 0 0 scale = 1.0 } structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 1/3. quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { use_asu_masks = True solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4.0 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True ignore_hydrogens = True } output { format = *mtz cns label = FMODEL type = real *complex file_name = None } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 } }

1 0

occupancy refinement
by Christian Roth 27 Jan '10

27 Jan '10

Dear all, I refine a structure of a protein to 1.4 A and found a few SO4-Ions. I tried to refine this sulfurs and some of these seems to be not fully occupied, as the negative difference density suggest. I tried to refine the occupancy of the sulfate ions to get an idea how strong the different binding sites might be occupied. All sulfate ions are in Chain C of my pdb. I tried to refine the occupancy individually using refine.occupancy.individual SO4 but this lead to different occupnacies for every atom for every atom and theix cant be the case for sure. Then I tried and group occupancy with resname=SO4 but now every sulfate ion has the same occupancy, which is indicated from my previous refinements also not the case, because two ions have no negative difference density. At the momentI can not figure out how I should combine the keywords for the individual occupancy refinement of the different sulfate ions. In my structure. Should I define for every ion a different chain or how I could overcome this problem? I would be very happy if anyone has a idea to sove this problem or tell me what keyword I misunderstood in the documentation. Best regards Christian

5 6

GUI for Auto-MR
by Laurie Betts 27 Jan '10

27 Jan '10

I installed version PHENIX 1-5-2 under Linux, and the main GUI has an option for AutoMR Phaser that says (old PHENIX GUI) - if that crashes is it because we don't have the old GUI installed? THe other main items seem to work fine. The last error message in the terminal window seems to suggest that is the case.... Thx, Laurie BEtts

2 1

twin data set
by r n 26 Jan '10

26 Jan '10

Hi I did processed a data set, which seems P3. I did molecular replacement and end up with solution with higher R factor. Then, I did used xtriage to check the data, it gave me possible space group P321 and few twin laws, this space group did not given me any solution , data seems have translation symmetry along z axis? Also I did processed in P1 and did molecular replacement end up in high R-factor. I really appreciate if any one has any suggestion what is going on with data? I given log file from xtriage, --------------------------------------------------------------------------------------------- | Point group | mean R_used | max R_used | mean R_unused | min R_unused | BIC | choice | ---------------------------------------------------------------------------------------------- | P 3 | None | None | 0.314 | 0.027 | 8.149e+03 | | | P 6 2 2 | 0.314 | 0.460 | None | None | 1.856e+05 | | | P 3 2 1 | 0.027 | 0.027 | 0.446 | 0.432 | 5.667e+03 | <--- | | P 6 | 0.432 | 0.432 | 0.249 | 0.027 | 1.856e+05 | | | P 3 1 2 | 0.460 | 0.460 | 0.242 | 0.027 | 1.859e+05 | | ---------------------------------------------------------------------------------------------- Statistics depending on twin laws ------------------------------------------------------------------ | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ------------------------------------------------------------------ | -h,-k,l | M | 0.432 | -0.009 | 0.046 | 0.022 | | h,-h-k,-l | M | 0.027 | 0.450 | 0.478 | 0.478 | | -k,-h,-l | M | 0.460 | -0.012 | 0.049 | 0.022 | ------------------------------------------------------------------ Patterson analyses - Largest peak height : 34.261 (corresponding p value : 7.017e-04)

1 0

map averaging
by Gabriela Guédez 25 Jan '10

25 Jan '10

Hi dear Phenixbb, Is there a command tool to make ncs density averaging in a high oligomerization model that has some maps clearer than others? not multi-crystal but the same crystal. Thank you, Gabriela -- ---------------------------------------------------------------------- Gabriela Guédez R. gabriela.guedez(a)bzh.uni-heidelberg.de

2 1

how to convert .cif with multiple datasets
by Zheng Zhou 24 Jan '10

24 Jan '10

Dear phenix experts: I am using phenix.cif_as_mtz to convert a .cif file downloaded from pdb, but when I run ################################################ phenix.cif_as_mtz XXXX-sf.cif Sorry: Crystal symmetry is not defined. Please use the --symmetry option. ################################################ Then I run ############################################### phenix.cif_as_mtz XXXX-sf.cif --symmetry=XXXX.pdb Multiple data sets found => ignored: XXXX-sf.cif What should I do? Thanks for your help. Joe

2 1