- phenixbb - phenix-online.org

data used in refinement
by Karolina Michalska 01 Feb '10

01 Feb '10

Hi all, I have a question concerning number of reflections used in refinement. In the phenix.refine log I can find a table saying that there are 34314 reflections in a work set and 1104 in a free set. This is in agreement with what Refmac prints out to pdb file under REMARK 3 (DATA USED IN REFINEMENT). However, the same remark in the pdb file produced by phenix.refine says there are 35404, which is neither a work set nor a sum of work and test sets. It is almost the latter option but still 14 reflections are missing and I cannot find in the log file what happened with them. Can anyone help me here? Karolina

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auto-open MTZ scheme
by Paul Emsley 29 Jan '10

29 Jan '10

Dear Phenixers, Prompted by Randy Read, Kevin and I have agreed that Coot should be able to auto-open MTZ files with columns labelled groupname.F_phi.F and groupname.F_phi.phi and groupname.DF_phi.DF, groupname.DF_phi.phi for difference maps for any value of groupname, of course. (Any weights should be applied to Fs before writing the file). We were wondering what the Phenix community/developers thought about that idea (there's not much point in adding this feature if you don't agree). Thanks, Paul.

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For your consideration: Table 1
by SIPPEL,KATHERINE H 29 Jan '10

29 Jan '10

Dear PHENIX programmers, I would like to preface this comment by saying that I love your suite of programs. I have converted to a 100% PHENIX fan girl and am dragging the rest of my lab down with me. I realize that you have a lot on your plates right now, what with all the bug fixes, updates, and bulletin board troubleshooting that you do. I am also primarily a biologist and have no comprehension of the effort required to keep everything running, but I do have a suggestion/request. I was putting the finishing touched on the first draft of a manuscript today and thought to myself, wouldn't it me wonderful if PHENIX could generate that all important crystallographic Table 1. You know the one that I am talking about with the data and refinement statistics. I am thinking a combination of PDB_EXTRACT and MOLEMAN where you input the log files from scaling and refinement and it outputs a handy-dandy test file with "parameter<tab>number that could easily be imported into your favorite spreadsheet (Open Office or Excel). I envision an interface with check boxes for the parameters you want to include and a place were you could input the resid of ligands for atom and b-factor counts. Like I said it is just a suggestion, in case you find yourselves bored and with time on your hands. Thanks for your time, Katherine -- SIPPEL,KATHERINE H Ph. D. candidate McKenna Lab Department of Biochemistry and Molecular Biology College of Medicine University of Florida

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phenix.pdbtools and anomalous?
by Kay Diederichs 28 Jan '10

28 Jan '10

Hi, I like the way I can obtain Fcalc with phenix.pdbtools --f-model. However I need to have the anomalous signal as well, for certain atoms, and a given wavelength. This does not seem to be possible with phenix.pdbtools. Is there a way to do this with phenix.refine ? thanks, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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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

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

28 Jan '10

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Using LigandFit to identify unknown density
by Katya Heldwein 27 Jan '10

27 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

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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

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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 } }

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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

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