Hi Brian
Thanks for the info
It’s what I was worried about.
In this case I am lucky in that my sequence starts at 1.
It does seem unfortunate that NMR users have to enter all the data manually.
- David
Associate Prof.
Dept of Pharmacology
CU School of Medicine.
Sent from my iPhone.
Please excuse brevity and typos
On Dec 7, 2018, at 2:38 AM, Brian Smith <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hi David,
OneDep currently does not handle the ECI NMRStar output metadata and does not really parse NMRStar properly even for the most basic info such as chemical shifts. This means that NMR spectroscopists depositing to the PDB have to enter all the metadata by hand. I have raised this with Aleks Gutmanas and I would recommend that as many people as can make their opinion on this matter known.
Brian Smith
PS. if your sequence numbering does not start at 1 and your are having trouble getting OneDep to match your chemical shifts to your coordinates, the key info to note is that your Comp_index_ID tags in your NMRStar file should be set to match your residue numbering (whereas it should really be the Auth_seq_ID tags). This can be achieved relatively easily for a single chain system in python with PyNMRSTAR something like (thanks to Jon Wedell at BMRB for this):
-------------
import pynmrstar
entry = pynmrstar.Entry.from_file('<your_input_file>.str')
shift_loops = entry.get_loops_by_category('_Atom_chem_shift')
for chemical_shift_loop in shift_loops:
chemical_shift_loop.sort_rows('Comp_Index_ID') # Sort the rows based on the existing Comp_index_ID
chemical_shift_loop.renumber_rows('ID', 1, False) # Fix the ID tag since we rearranged the rows
chemical_shift_loop.renumber_rows('Comp_index_ID', <your_seq_start>, True) # Renumber the Comp_index_ID
entry.write_to_file('<your_fixed_output_file>.str')
--------------
Note that this is only a partial fix - as it only adjusts the chemical shift loop(s), the NMRStar file will no longer be self consistent - but will allow you to get into OneDep.
Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
College of Medical, Veterinary & Life Sciences,
Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089
----------------------------------------------------------------------
The University of Glasgow, charity number SC004401
________________________________________
From: CcpNmr software mailing list [[log in to unmask]<mailto:[log in to unmask]>] on behalf of Jones, David (Pharm) [[log in to unmask]<mailto:[log in to unmask]>]
Sent: 07 December 2018 05:55
To: [log in to unmask]<mailto:[log in to unmask]>
Subject: ECI and OneDep PDB Deposition
Hi All
Can the ECI deposition be used with the OneDep deposition system,.
I cannot find any mention of this since the AutoDep system was retired.
Thanks
David Jones
Dept. of Pharmacology,
University of Colorado School of Medicine
Tel. +1 303 724 3600
http://pharmacology.ucdenver.edu/faculty/jones
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