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
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: [email protected] [[email protected]] on behalf of Zhang yu [[email protected]] Sent: Sunday, February 19, 2012 4:42 PM To: [email protected] 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
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
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:* [email protected] [ [email protected]] on behalf of Zhang yu [ [email protected]] *Sent:* Sunday, February 19, 2012 4:42 PM *To:* [email protected] *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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
Hi, or alternatively: phenix.map_box model.pdb map_coefficients.mtz selection="chain A" will create a box with map and model in it. The output will be a pdb file with the chain A, and a map in a box around chain A output in three different formats: X-plor, MTZ file with map coefficients and CCP4 map. Pavel On 2/19/12 3:46 PM, Terwilliger, Thomas C wrote:
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:* [email protected] [[email protected]] on behalf of Zhang yu [[email protected]] *Sent:* Sunday, February 19, 2012 4:42 PM *To:* [email protected] *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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Pavel Afonine -
Terwilliger, Thomas C -
Zhang yu