Dear Tom,

Thanks. This is waht I need.

Questions, I am able to run the command, but couldn' get output files (cutout.mtz and cutout.pdb). I pasted the eff and log files as below,

*.eff
cutout {
  input_files {
    pdb_in = "********refine_25-omit_nt.pdb"
    mtz_in = "********refine_25.mtz"
    pdb_to_restore_position = None
  }
  output_files {
    mtz_out = "cutout.mtz"
    pdb_out = "cutout.pdb"
    pdb_restored_in_position = None
    log = "cutout.log"
    params_out = "cutout_params.eff"
  }
  directories {
    temp_dir = "temp_dir"
    output_dir = ""
  }
  cutout_region {
    high_resolution = None
    cutout_center = None
    cutout_dimensions = 15 15 15
    padding = 5
    cutout_type = *box sphere model
    cutout_sphere_radius = 10
    cutout_model_radius = 5
    cutout_subtract_mean = False
    atom_selection = None
  }
  control {
    verbose = False
    raise_sorry = False
    debug = False
    dry_run = False
    resolve_command_list = None
  }
}


*.log

#                       cutout
#
# Cut out density from a map


# Type phenix.doc for help
Cutting out density
Miller arrays in mtz_in: ['H', 'K', 'L', 'F-obs(+)', 'SIGF-obs(+)', 'F-obs(-)', 'SIGF-obs(-)', 'R-free-flags', 'F-obs-filtered(+)', 'SIGF-obs-filtered(+)', 'F-obs-filtered(-)', 'SIGF-obs-filtered(-)', 'F-model(+)', 'PHIF-model(+)', 'F-model(-)', 'PHIF-model(-)', '2FOFCWT', 'PH2FOFCWT', '2FOFCWT_no_fill', 'PH2FOFCWT_no_fill', 'FOFCWT', 'PHFOFCWT', 'ANOM', 'PANOM']
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Setting FP and PHI from map_coeffs
Center of cutout region will be from model center at:  [6.6284972467757814, -0.726900775249967, 70.35264573974781]

************************************************


************************************************



2012/2/19 Terwilliger, Thomas C <terwilliger@lanl.gov>
Hi Yu Zhang,

You can use the tool "phenix.cut_out_density" to select density from a map within a radius you define of atoms in a PDB file that you supply.  I hope that helps!

All the best,
Tom T

From: phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Zhang yu [phenixzyfish@gmail.com]
Sent: Sunday, February 19, 2012 4:42 PM
To: phenixbb@phenix-online.org
Subject: [phenixbb] FFT map coefficients only for certain chains

Dear Phenixers,

Is that possible to generate map coefficients only for certain chains? For example, I have two chains, A and B, and I would like to output a map file only contains coefficients for chain A. The "isomesh" command in Pymol could generate similar images. But my purpose is not for presentation, I need a map file only contains coefficient for certain chains.

In the interface of "FFT" tool in Phenix or CCP4, there is an option to include a PDB file and define atom selections. It describe that "If a PDB is supplied, the output map will cover the model plus a buffer on all sides. The atom selection parameters can be used to specify a smaller region" . If I define the selection as chain A when I run the FFT, the output map still covers a rectangular block containing chain A, instead of regions only surrounding chain A.

Thanks.

Yu Zhang

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