Subject: Re: [nmr_sparky] sparky spectrum list assigned residue names split
From: Woonghee Lee
Date: Apr 8, 2019

Previous: 1456

Yes. I think find replace in a text editor is even essier option.
Woonghee

On Mon, Apr 8, 2019, 08:29 Schröder, David Christopher dschroeder@... [nmr_sparky] nmr_sparky@yahoogroups.com wrote:
 

Hi Eiso,

thanks for your answer. I used the at- dialog.

However for Group I chose a combination of the three letter

residue name followed by the residue number. My used residue names

could be standard 3 Letter amino acid code but also A4n A4c where the first letter is derived form

1 Letter amino acid code second character is a digit (defining the triazole connectivity 4 or 5)

and the third character is a Letter c or n defining C or N terminal position to the triazole).

So A4n is an Alanine residue N-terminal to a 1-4, disubstituted triazole replacing the standard amide bond.

In addition T14 and T15 is the 1-4 ore 1-5, triazole tring as residue.

All this was from a force field definition.

 

So as Woonghee answered how sparky splits,  it will be easier to either use standard 3 Letter code in sparky assignements, export the

spectrum list and replace it after words by search and replace or the write a python script to convert from the sparyk assignment column to multi column (Res. Number / res. Name / Atom name).

 

Best regards,

David

 

 

 

Von: nmr_sparky@yahoogroups.com nmr_sparky@yahoogroups.com
Gesendet: Montag, 8.
April 2019 14:38
An: nmr_sparky@yahoogroups.com
Betreff: Re: [nmr_sparky] sparky spectrum list assigned residue names split

 

 

Hi David,

its not entirely clear (to me at least) what your trying to do but nomenclature
in sparky works
more or less like this:

theres a group name (residue)   e.g.    A7   Ala7   HYP25 V25a V25b etc.
so a name, number and optional variant .   [A-Z]+[0-9]+[a-z]*

and there are atom names, e.g.  HA HB2 H343 CZ  QD (pseudo atom representing
HD1,HD2) MB (methyl: HB1 HB2HB3)

These are the things you should fill in for group and atom if you for
example assign something via the at dialog.

Sparky in general doesnt enforce this nomenclature though.

btw I dont understand what this is supposed to mean:
  7 ALA HA; 18 V4n HB etc
7 ALA HA is clear enough but what is 18 V4n HB ?



Eiso





Schröder, David Christopher
dschroeder@... [nmr_sparky] wrote:

Dear all,

I am using sparky as a beginner to assign small modified peptides(peptide
bonds replaced by triazoles). Therefor

I used our pdb nomenclature for assignments. All my residue names consist of
three characters followed by the residues number.

E.g. ALA7 V4n18 L4c22. For the NOESY spectrum list I would like to have it
split accordingly: 7 ALA HA; 18 V4n HB etc. However it splits prior the

first number instead of three letters. Is there a possibility to define
artificial residue names?

Best regards,

David