Dear Tom,<br><br>Thanks. This is waht I need.<br><br>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,<br><br><font size="4">*.eff </font><br>
cutout {<br> input_files {<br> pdb_in = "********refine_25-omit_nt.pdb"<br> mtz_in = "********refine_25.mtz"<br> pdb_to_restore_position = None<br> }<br> output_files {<br> mtz_out = "cutout.mtz"<br>
pdb_out = "cutout.pdb"<br> pdb_restored_in_position = None<br> log = "cutout.log"<br> params_out = "cutout_params.eff"<br> }<br> directories {<br> temp_dir = "temp_dir"<br>
output_dir = ""<br> }<br> cutout_region {<br> high_resolution = None<br> cutout_center = None<br> cutout_dimensions = 15 15 15<br> padding = 5<br> cutout_type = *box sphere model<br> cutout_sphere_radius = 10<br>
cutout_model_radius = 5<br> cutout_subtract_mean = False<br> atom_selection = None<br> }<br> control {<br> verbose = False<br> raise_sorry = False<br> debug = False<br> dry_run = False<br> resolve_command_list = None<br>
}<br>}<br><br><br><font size="4">*.log <br></font><br># cutout<br>#<br># Cut out density from a map<br><br><br># Type phenix.doc for help<br>Cutting out density<br>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']<br>
Setting FP and PHI from map_coeffs<br>Setting FP and PHI from map_coeffs<br>Setting FP and PHI from map_coeffs<br>Setting FP and PHI from map_coeffs<br>Center of cutout region will be from model center at: [6.6284972467757814, -0.726900775249967, 70.35264573974781]<br>
<br>************************************************<br><br><br>************************************************<br><br><br><br><div class="gmail_quote">2012/2/19 Terwilliger, Thomas C <span dir="ltr"><<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>></span><br>
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<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Yu Zhang,
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<div>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!</div>
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<div>All the best,</div>
<div>Tom T</div>
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<div style="direction:ltr"><font color="#000000" face="Tahoma"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>] on behalf of Zhang yu [<a href="mailto:phenixzyfish@gmail.com" target="_blank">phenixzyfish@gmail.com</a>]<br>
<b>Sent:</b> Sunday, February 19, 2012 4:42 PM<br>
<b>To:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> [phenixbb] FFT map coefficients only for certain chains<br>
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<div>Dear Phenixers,<br>
<br>
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.
<br>
<br>
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.<br>
<br>
Thanks.<br>
<br>
Yu Zhang<br>
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