Peaklist preparation for eNOE pipeline - Revision history

Dima: /* Transfer of assignments to the NMRpipe peaks */

2022-04-08T07:45:38Z

Transfer of assignments to the NMRpipe peaks

← Older revision		Revision as of 09:45, 8 April 2022
Line 40:		Line 40:
	pip install argparse		pip install argparse
	pip install matplotlib		pip install matplotlib

			This step has to be done only once. When you are finished with python scripts you can deactivate it
			deactivate

			And next time you can activate it again
			source venv/bin/activate

	Copy the peaked peaks to the 03-Assignment/ folder. Copy the assigned NOESY peaklist to the same folder. Save the transfer [[Media:Transfer.zip\|script]] and execute it sequentially for the backbone, aliphatic and aromatic protons.		Copy the peaked peaks to the 03-Assignment/ folder. Copy the assigned NOESY peaklist to the same folder. Save the transfer [[Media:Transfer.zip\|script]] and execute it sequentially for the backbone, aliphatic and aromatic protons.

Dima: /* NMRpipe peak peaking */

2022-04-08T07:18:18Z

NMRpipe peak peaking

← Older revision		Revision as of 09:18, 8 April 2022
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	==== NMRpipe peak peaking ====		==== NMRpipe peak peaking ====
	Peak the nitrogen region, aliphatic carbon region and aromatic carbon region of the NOESY with highest mixing time with NMRpipe. ~~Adjust~~ the ~~crop~~ by adjusting the threshold such, that the total number of peaks is 3 to 5 times larger than the number of peaks ~~provided by ARTINA~~ (because NMRpipe also peaks water and a lot of "false positives" along the diagonal, peak even more for the aromatic peaks as they are highly diluted by backbone nitrogen peaks). Save the peaks as '''N15NOESY.tab''', '''C13NOESY_@ALI.tab''' and '''C13NOESY_@ARO.tab''' in the 02-PeakPeaking/ folder.		Peak the nitrogen region, aliphatic carbon region and aromatic carbon region of the NOESY with highest mixing time with NMRpipe. Optimize the number of the peaked peaks by adjusting the threshold such, that the total number of peaks is 2 to 5 times larger than the number of peaks in previously manually or automatically generated NOESY assignment (because NMRpipe also peaks water and a lot of "false positives" along the diagonal, peak even more for the aromatic peaks as they are highly diluted by backbone nitrogen peaks). Save the peaks as '''N15NOESY.tab''', '''C13NOESY_@ALI.tab''' and '''C13NOESY_@ARO.tab''' in the 02-PeakPeaking/ folder.

	==== Transfer of assignments to the NMRpipe peaks ====		==== Transfer of assignments to the NMRpipe peaks ====

Dima: /* Transfer of assignments done by ARTINA to the NMRpipe peaks */

2022-04-08T07:15:40Z

Transfer of assignments done by ARTINA to the NMRpipe peaks

← Older revision		Revision as of 09:15, 8 April 2022
Line 29:		Line 29:
	Peak the nitrogen region, aliphatic carbon region and aromatic carbon region of the NOESY with highest mixing time with NMRpipe. Adjust the crop by adjusting the threshold such, that the total number of peaks is 3 to 5 times larger than the number of peaks provided by ARTINA (because NMRpipe also peaks water and a lot of "false positives" along the diagonal, peak even more for the aromatic peaks as they are highly diluted by backbone nitrogen peaks). Save the peaks as '''N15NOESY.tab''', '''C13NOESY_@ALI.tab''' and '''C13NOESY_@ARO.tab''' in the 02-PeakPeaking/ folder.		Peak the nitrogen region, aliphatic carbon region and aromatic carbon region of the NOESY with highest mixing time with NMRpipe. Adjust the crop by adjusting the threshold such, that the total number of peaks is 3 to 5 times larger than the number of peaks provided by ARTINA (because NMRpipe also peaks water and a lot of "false positives" along the diagonal, peak even more for the aromatic peaks as they are highly diluted by backbone nitrogen peaks). Save the peaks as '''N15NOESY.tab''', '''C13NOESY_@ALI.tab''' and '''C13NOESY_@ARO.tab''' in the 02-PeakPeaking/ folder.

	==== Transfer of assignments ~~done by ARTINA~~ to the NMRpipe peaks ====		==== Transfer of assignments to the NMRpipe peaks ====
	Create a fresh python environment		Create a fresh python environment
	python -m venv venv		python -m venv venv

Dima at 07:15, 8 April 2022

2022-04-08T07:15:11Z

← Older revision		Revision as of 09:15, 8 April 2022
Line 3:		Line 3:
	In summary, our approach consists of following steps:		In summary, our approach consists of following steps:
	# NMRpipe peak peaking		# NMRpipe peak peaking
	# Transfer of assignments ~~done by ARTINA~~ to the NMRpipe peaks		# Transfer of manual or automatically generated assignments to the NMRpipe peaks
	# Sequential assignment of NOESY spectra with different mixing times using NMRpipe		# Sequential assignment of NOESY spectra with different mixing times using NMRpipe

Line 11:		Line 11:
	# CYANA		# CYANA
	# Python3		# Python3
	~~# UCSF Chimera~~
	# PDBcor. In case if PDBcor is not yet installed, please go to this [https://github.com/dzmitryashkinadze/PDBCor link] and follow installation instructions. Later we will refer to the PDBcor installation path as '''PATH/To/PDBcor'''

	==== Data preparation ====		==== Data preparation ====

Dima at 07:14, 8 April 2022

2022-04-08T07:14:15Z

← Older revision		Revision as of 09:14, 8 April 2022
Line 1:		Line 1:
	In this tutorial we will ~~calculate~~ the ~~exact NOE multi-state calculation of~~ the ~~protein~~ of ~~interest (POI,~~ spectra ~~are not supplied~~) from ~~ARTINA outputs (not covered in this tutorial)~~.		In this tutorial we will prepare the input data for the eNOE pipeline (assigned series of NOESY spectra with different mixing times) from manually / automatically generated assignments of a single NOESY spectrum.

	In summary, our approach consists of following steps:		In summary, our approach consists of following steps:

Dima: moved Exact NOE multi-state structure calculation using ARTINA to Peaklist preparation for eNOE pipeline

2022-04-08T07:10:25Z

moved Exact NOE multi-state structure calculation using ARTINA to Peaklist preparation for eNOE pipeline

← Older revision	Revision as of 09:10, 8 April 2022
(No difference)

Dima: Created page with "In this tutorial we will calculate the exact NOE multi-state calculation of the protein of interest (POI, spectra are not supplied) from ARTINA outputs (not covered in this tu..."

2022-04-07T16:31:26Z

Created page with "In this tutorial we will calculate the exact NOE multi-state calculation of the protein of interest (POI, spectra are not supplied) from ARTINA outputs (not covered in this tu..."

New page

In this tutorial we will calculate the exact NOE multi-state calculation of the protein of interest (POI, spectra are not supplied) from ARTINA outputs (not covered in this tutorial).

In summary, our approach consists of following steps:
# NMRpipe peak peaking
# Transfer of assignments done by ARTINA to the NMRpipe peaks
# Sequential assignment of NOESY spectra with different mixing times using NMRpipe

==== Software installation ====

This tutorial requires following software:
# CYANA
# Python3
# UCSF Chimera
# PDBcor. In case if PDBcor is not yet installed, please go to this [https://github.com/dzmitryashkinadze/PDBCor link] and follow installation instructions. Later we will refer to the PDBcor installation path as '''PATH/To/PDBcor'''

==== Data preparation ====
Create the root project folder tutorial/
mkdir tutorial
cd tutorial
mkdir 01-Spectra
mkdir 02-PeakPeaking
mkdir 03-Assignment
mkdir 04-Series
mkdir 05-eNORA
mkdir 06-SingleState
mkdir 07-MultiState

Process all NOESY mixing times and save them in separate folders in 01-Spectra/ folder.

==== NMRpipe peak peaking ====
Peak the nitrogen region, aliphatic carbon region and aromatic carbon region of the NOESY with highest mixing time with NMRpipe. Adjust the crop by adjusting the threshold such, that the total number of peaks is 3 to 5 times larger than the number of peaks provided by ARTINA (because NMRpipe also peaks water and a lot of "false positives" along the diagonal, peak even more for the aromatic peaks as they are highly diluted by backbone nitrogen peaks). Save the peaks as '''N15NOESY.tab''', '''C13NOESY_@ALI.tab''' and '''C13NOESY_@ARO.tab''' in the 02-PeakPeaking/ folder.

==== Transfer of assignments done by ARTINA to the NMRpipe peaks ====
Create a fresh python environment
python -m venv venv
Activate it
source venv/bin/activate
Install necessary packages
pip install numpy
pip install pandas
pip install tqdm
pip install argparse
pip install matplotlib

Copy the peaked peaks to the 03-Assignment/ folder. Copy the assigned NOESY peaklist to the same folder. Save the transfer [[Media:Transfer.zip|script]] and execute it sequentially for the backbone, aliphatic and aromatic protons.
python convert.py /path/to/tutorial/03-Assignment/N15NOESY.tab /path/to/tutorial/03-Assignment/N15NOESY_@POS_@FLYA_asn.peaks N
python convert.py /path/to/tutorial/03-Assignment/C13NOESY_@ALI.tab /path/to/tutorial/03-Assignment/C13NOESY_@ALI_@FLYA_asn.peaks C_@ALI
python convert.py /path/to/tutorial/03-Assignment/C13NOESY_@ARO.tab /path/to/tutorial/03-Assignment/C13NOESY_@ARO@NEG_@FLYA_asn.peaks C_@ARO --w1_shift=HEAVY_ATOM_SPECTRAL_WIDTH_IN_PPM

Change the path/to/tutorial and HEAVY_ATOM_SPECTRAL_WIDTH_IN_PPM to the actual path and spectral width in heavy atom value.

This will create assigned NMRpipe tab files '''N15NOESY_asn.tab''', '''C13NOESY_@ALI_asn.tab''' and '''C13NOESY_@ARO_asn.tab''' in the 03-Assignment/ folder.

For quality control check that histograms of CYANA vs Pipe overlap for all 3 dimensions (for example file N_W1_overlay.png shows overlap between CYANA and Pipe shift histograms in the first dimensions for the nitrogen region of the NOESY).

==== Sequential assignment of NOESY spectra with different mixing times using NMRpipe ====
Copy assigned NMRpipe tab files to the 04-Series/ folder.

Create the NMRpipe script series3D_N.com for sequential assignment of the nitrogen spectrum with following content:
#!/bin/csh
set DX = 1
set DY = 3
set DZ = 2
set specList = (path/to/tutorial/01-Spectra/X/ft/HCNHnoesyHdirH%03d.ft3 path/to/tutorial/01-Spectra/Y/ft/HCNHnoesyHdirH%03d.ft3 path/to/tutorial/01-Spectra/Z/ft/HCNHnoesyHdirH%03d.ft3)
set inName = N15NOESY_asn.tab
echo -----------------------------------------------
echo Performing analysis by Fourier interpolation.
echo Updated peak table will be series.tab
echo
/bin/rm -f series.list
foreach i ($specList)
echo $i >> series.list
end
seriesTab -in $inName -list series.list -ndim 3 \
-out series.tab -dx $DX -dy $DY -dz $DZ \
-xzf 64 -yzf 64 -zzf 64 -adx 0 -ady 0 -adz 0 -max -verb

Change the path to the spectra such that X, Y, Z are spectra ordered from highest to lowest mixing times. If necessary, add additional entries.

Run the series script
csh
prepare nmrPipe
./series3D_N.com

This will create the series.tab file. Rename it to the series_N.tab and remove 2 lines from the header:
NULLVALUE -666
NULLSTRING *

Repeat this step for the aliphatic and aromatic protons. Combine all 3 series in series_all.tab files by keeping only one header. This combined series file can be directly used for [[ENORA and multi-state structure calculations]].