April 2011 - phenixbb - phenix-online.org

phenix.maps2mtz
by Yarrow Madrona 03 Apr '11

03 Apr '11

Hello, I am running phenix-1.7-650 and would like to generate a ccp4 map for use in pymol from an mtz. I can type: phenix.maps2mtz file.mtz but I cannot figure out how to limmit the selection to a single chain (chain A). I guess you can do this in maps.params but I wanted to keep it simple without having to use the sca file. Thank you. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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"FOM" or HL coeffs from model?
by Phoebe Rice 01 Apr '11

01 Apr '11

How can I get phenix to spit out not just PhiModel but an estimated FOM or fake HL coefficients (without experimental phases - just based on how badly my model agrees with FOBS)? And I'd like the weights in their own personal mtz column(s), not just precombined in a "weighted phi" column. In case anybody cares why, I'd like to use solvent massaging and domain-wise averaging to remove bias from a low-resolution model-phased map, preferably with DM, unless anybody has a better suggestion. I did rigid body, TLS, etc on the model in phenix, so it seems like phenix has already calculated all the info I want if I could only squeeze it out. thanks, Phoebe ===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alph… http://www.rsc.org/shop/books/2008/9780854042722.asp

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phenix.reciprocal_space_arrays: a new command line tool to get Fcalc, Fbulk, Fmask, FOM, HL, and more all in one MTZ file
by Pavel Afonine 01 Apr '11

01 Apr '11

PHENIX users: just a quick notice: starting PHENIX nightly build version dev-717 and up, a new command line tool phenix.reciprocal_space_arrays will be available. This tool takes a PDB model and a data file (in most of commonly used formats: MTZ, CNS, SHELX,...) and outputs a MTZ file containing a number of arrays that are typically used in various crystallographic calculations, such as R-factors, maps, refinement targets, etc. The output arrays include: Fmodel, Fcalc, Fmask, Fbulk, FOM, resolution, HL(input original, computed from model and combined), FB_CART (overall anisotropic scale), input Fobs and Rfree-flags and more. To run: phenix.reciprocal_space_arrays model.pdb data.mtz To see the result: phenix.mtz.dump output_file.mtz Please let me know should you have any questions, suggestions or simply find a bug! Pavel.

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low resolution map weirdness with newer releases
by Scott Classen 01 Apr '11

01 Apr '11

Something changed between build 432 and 486 that made my low resolution maps look much crappier. See attached tiff. See if you can guess which map was produced by the release 486. def file looks more or less like this (from a --diff-params): refinement { crystal_symmetry { unit_cell = top secret space_group = top secret } input { pdb { file_name = "../4_23_003.pdb" } xray_data { file_name = "../4_23.sca.mtz" labels = "4_23.sca,SIG4_23.sca" high_resolution = 3.9 r_free_flags { file_name = "../4_23.sca.mtz" label = "R-free-flags" test_flag_value = 1 } } } output { prefix = "test-486" serial = 1 } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ individual_adp group_adp tls occupancies group_anomalous sites { individual = "chain A and resseq 100:107" individual = "chain B and resseq 500:507" individual = "chain E and resseq 100:107" individual = "chain F and resseq 500:507" individual = "chain C and resseq 111:117" individual = "chain D and resseq 111:117" individual = "chain G and resseq 111:117" individual = "chain H and resseq 111:117" individual = "chain C and resseq 63:68" individual = "chain D and resseq 63:68" individual = "chain G and resseq 63:68" individual = "chain H and resseq 63:68" rigid_body = "chain A" rigid_body = "chain B" rigid_body = "chain C" rigid_body = "chain D" rigid_body = "chain E" rigid_body = "chain F" rigid_body = "chain G" rigid_body = "chain H" } } main { number_of_macro_cycles = 1 secondary_structure_restraints = True random_seed = 3141766 optimize_mask = False } modify_start_model { adp { set_b_iso = 50 } } fake_f_obs { mask { ignore_hydrogens = True } } geometry_restraints.edits { excessive_bond_distance_limit = 20 } mask { ignore_hydrogens = True } simulated_annealing { start_temperature = 300 final_temperature = 200 } target_weights { wxc_scale = 0.4 } ias { b_iso_max = 60 } secondary_structure { h_bond_restraints { substitute_n_for_h = True remove_outliers = False sigma = 0.02 h_o_distance_ideal = 2.95 h_o_distance_max = 5 n_o_distance_ideal = 2.95 n_o_distance_max = 5 } }

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omit map
by intekhab alam 01 Apr '11

01 Apr '11

Hi i generated an iterative build omit map using phenix and the output fule that i got is resolve_composite_map.mtz, but i cannot open this file in coot, what modifications do ineed to open this file in coot. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

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