Hi Yu Zhang,
I'm sorry, yes it looks like something didn't work all right. It is possible that cut_out_density ran out of memory in this job, which would mean you might get it to run with
high_resolution = 2.5
If this option is not present in your version then a more recent version will have this (and will possibly fix the out of memory problem as well). I think that you want the option
cutout_type = box sphere *model
from what you describe as well. If these do not fix the problem, then if you would like to send me the map and model off-line, then I will be happy to debug the problem.
All the best,
Tom T
________________________________
From: [email protected] [[email protected]] on behalf of Zhang yu [[email protected]]
Sent: Sunday, February 19, 2012 5:13 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] FFT map coefficients only for certain chains
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