Gd-Lysozyme - Revision history

Tara: /* Solve the structure */

2014-10-06T21:55:24Z

Solve the structure

← Older revision		Revision as of 21:55, 6 October 2014
Line 701:		Line 701:

	libtbx.python [[map_height_at_atoms.py]] \		libtbx.python [[map_height_at_atoms.py]] \
	~~Gd-Lysozyme_mark0_refine_28~~.pdb GdLysozymeanom_4etc_s0_mark0.mtz \		001_001.pdb GdLysozymeanom_4etc_s0_mark0.mtz \
	selection="element GD"		selection="element GD"
	input.xray_data.labels=Iobs \		input.xray_data.labels=Iobs \
	xray_data.r_free_flags.file_name=~~reflections~~.mtz \		xray_data.r_free_flags.file_name=001_data.mtz \
	xray_data.r_free_flags.label=~~FreeR_flag~~		xray_data.r_free_flags.label=R-free-flags

	Promising results for the two Gd sites:		Promising results for the two Gd sites:
	<pre>		<pre>
	pdb="GD GD A 201 " : 19.16 sigma		pdb="GD GD A 201 " : 17.85 sigma
	pdb="GD GD A 202 " : 24.09 sigma		pdb="GD GD A 202 " : 23.46 sigma

	</pre>		</pre>

2014-10-06T21:49:07Z

Solve the structure

← Older revision		Revision as of 21:49, 6 October 2014
Line 696:		Line 696:


	RWORK = 20.4% RFREE = 25.3% out to 1.9 Angstrom		RWORK = 20.25% RFREE = 23.7% out to 1.9 Angstrom

	Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers.		Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers.

2014-10-06T21:39:18Z

Solve the structure

← Older revision		Revision as of 21:39, 6 October 2014
Line 682:		Line 682:


	Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb		Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb and extending the resolution from 1.5 - 100 using phenix
			(new R-free-flags file is reflections.mtz)
			generate restraints for the "DO3" ligands using phenix.elbow

	Refine the model		Refine the model

2014-10-06T21:33:23Z

Solve the structure

← Older revision		Revision as of 21:33, 6 October 2014
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	xray_data.r_free_flags.label=FreeR_flag \		xray_data.r_free_flags.label=FreeR_flag \
	main.number_of_macro_cycles=7 optimize_xyz_weight=True \		main.number_of_macro_cycles=7 optimize_xyz_weight=True \
	optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=Iobs~~(+)~~,~~SIGIobs(+),Iobs(-),SIGIobs(-)~~, \		optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=Iobs unit_cell="78.033, 78.033, 38.833" \
	ordered_solvent=true ordered_solvent.mode=every_macro_cycle		ordered_solvent=true ordered_solvent.mode=every_macro_cycle

2014-10-06T20:41:51Z

Solve the structure

← Older revision		Revision as of 20:41, 6 October 2014
Line 705:		Line 705:
	xray_data.r_free_flags.label=FreeR_flag		xray_data.r_free_flags.label=FreeR_flag

	Promising results for the ~~Zn and one Ca~~:		Promising results for the two Gd sites:
	<pre>		<pre>
	pdb="ZN ZN A ~~317~~ " : 5.97 sigma		pdb="GD GD A 201 " : 19.16 sigma
	pdb="CA CA A ~~318~~ " : 0.~~93 sigma~~		pdb="GD GD A 202 " : 24.09 sigma
	~~pdb="CA CA A 319 " : 2.74 sigma~~
	~~pdb="CA CA A 320 " : 1.08 sigma~~
	~~pdb="CA CA A 321 " : 0.20 sigma~~
	~~</pre>~~

	~~Better results from trial 005:~~
	~~<pre>~~
	~~pdb="ZN ZN A 317 " : 7.66 sigma~~
	~~pdb="CA CA A 318 " : 1.10 sigma~~
	~~pdb="CA CA A 319 " : 2.52 sigma~~
	~~pdb="CA CA A 320 " : 1.40 sigma~~
	~~pdb="CA CA A 321 " : 1.01~~ sigma

	</pre>		</pre>

2014-10-06T20:09:59Z

Solve the structure

← Older revision		Revision as of 20:09, 6 October 2014
Line 700:		Line 700:
	libtbx.python [[map_height_at_atoms.py]] \		libtbx.python [[map_height_at_atoms.py]] \
	Gd-Lysozyme_mark0_refine_28.pdb GdLysozymeanom_4etc_s0_mark0.mtz \		Gd-Lysozyme_mark0_refine_28.pdb GdLysozymeanom_4etc_s0_mark0.mtz \
			selection="element GD"
	input.xray_data.labels=Iobs \		input.xray_data.labels=Iobs \
	xray_data.r_free_flags.file_name=reflections.mtz \		xray_data.r_free_flags.file_name=reflections.mtz \

2014-10-06T20:08:45Z

Solve the structure

← Older revision		Revision as of 20:08, 6 October 2014
Line 699:		Line 699:

	libtbx.python [[map_height_at_atoms.py]] \		libtbx.python [[map_height_at_atoms.py]] \
	~~001_001~~.pdb ~~thermoanom_2tli_s0_mark0~~.mtz \		Gd-Lysozyme_mark0_refine_28.pdb GdLysozymeanom_4etc_s0_mark0.mtz \
	input.xray_data.labels=Iobs \		input.xray_data.labels=Iobs \
	xray_data.r_free_flags.file_name=~~4ow3_original_iobs_flags~~.mtz \		xray_data.r_free_flags.file_name=reflections.mtz \
	xray_data.r_free_flags.label=~~R-free-flags~~		xray_data.r_free_flags.label=FreeR_flag

	Promising results for the Zn and one Ca:		Promising results for the Zn and one Ca:

2014-10-06T19:54:41Z

Solve the structure

← Older revision		Revision as of 19:54, 6 October 2014
Line 685:		Line 685:

	Refine the model		Refine the model
	phenix.refine 4n5r.pdb refinement.output.prefix=001 \		phenix.refine 4n5r.pdb [[DO3.cif]] refinement.output.prefix=001 \
	xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \		xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \
	xray_data.r_free_flags.file_name=reflections.mtz \		xray_data.r_free_flags.file_name=reflections.mtz \
	xray_data.r_free_flags.label=FreeR_flag \		xray_data.r_free_flags.label=FreeR_flag \
	main.number_of_macro_cycles=7 optimize_xyz_weight=True \		main.number_of_macro_cycles=7 optimize_xyz_weight=True \
	optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=~~IMEAN~~ \		optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=Iobs(+),SIGIobs(+),Iobs(-),SIGIobs(-), \
	ordered_solvent=true ordered_solvent.mode=every_macro_cycle		ordered_solvent=true ordered_solvent.mode=every_macro_cycle


	RWORK = 21.2% RFREE = 25.7% out to 1.9 Angstrom		RWORK = 20.4% RFREE = 25.3% out to 1.9 Angstrom

	Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers.		Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers.

2014-10-06T18:16:32Z

Solve the structure

← Older revision		Revision as of 18:16, 6 October 2014
Line 680:		Line 680:
	Use Gd-Lysozyme anomalous structure to get Gd sites:		Use Gd-Lysozyme anomalous structure to get Gd sites:
	phenix.fetch_pdb --mtz 4n5r		phenix.fetch_pdb --mtz 4n5r
	~~phenix.automr 4n5r.pdb GdLysozymeanom_4etc_s0_mark0.mtz seq_file=4n5r.fa identity=100 copies=1 build=False~~

	~~The MR-placed model is in ./AutoMR_run_1_/MR.1.pdb.~~

	Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb		Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb

	Refine the model		Refine the model

2014-10-06T18:10:42Z

Solve the structure

← Older revision		Revision as of 18:10, 6 October 2014
Line 689:		Line 689:
	phenix.refine 4n5r.pdb refinement.output.prefix=001 \		phenix.refine 4n5r.pdb refinement.output.prefix=001 \
	xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \		xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \
	xray_data.r_free_flags.file_name=~~4etc_original_iobs_flags~~.mtz \		xray_data.r_free_flags.file_name=reflections.mtz \
	xray_data.r_free_flags.label=FreeR_flag \		xray_data.r_free_flags.label=FreeR_flag \
	main.number_of_macro_cycles=6 optimize_xyz_weight=True \		main.number_of_macro_cycles=7 optimize_xyz_weight=True \
	optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=IMEAN \		optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=IMEAN \
	ordered_solvent=true ordered_solvent.mode=every_macro_cycle		ordered_solvent=true ordered_solvent.mode=every_macro_cycle