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Sshift subtracts the random coil chemical shift from your protein's HN, HA, CA, CB, or CO chemical shift.
The program is /nmr/dg/lib/randomcoil/sshift Ran program on Solaris operating system. Also runs on....
should be in "4-column format", eg, for alpha protons:
1 MET HA 4.07 2 ALA HA 3.97 3 SER HA 5.12 4 PRO HA 3.42
Glycine HA chemical shifts need to be listed something like the following:
6 GLY HA- 3.96 6 GLY HA+ 4.17
The program should also work with 'HA2' and 'HA3', so long as the two are different and start with 'HA'.
Other atom names are HN, CA, CB, CO
If you want the program to average your glycine HA proton chemical shifts for you, be sure to list your glycine HA protons as indicated above, and use the A=GLY:HA argument (see example below under 'Command Line').
The random coil chemical shifts and the corresponding literature references are found in /nmr/dg/lib/randomcoil/chemref
It is possible to apply a temperature correction for backbone amides by using the T=temp argument (temperature in K). One does obtain different output by setting T to different values, but the output file is misleading since it does not indicate that the correction has been applied. The output file reads: # no temperature correction at the moment
/nmr/dg/lib/randomcoil/sshift C=/nmr/dg/lib/randomcoil/chemref T=temp A=GLY:HA \ my.assmts > my.ss(You must actually type in "C=", "T=" (the point is that "X=" is part of the argument.)
eg)
/nmr/dg/lib/randomcoil/sshift C=/nmr/dg/lib/randomcoil/chemref A=GLY:HA \
my.alphas > my.alphas.ss
eg)
/nmr/dg/lib/randomcoil/sshift C=/nmr/dg/lib/randomcoil/chemref T=300 \
my.amides > my.amides.ss
Courtesy of Barbara Potts.