Chemical Shift Referencing Calculator

Below is the protocol I follow for chemical shift referencing (direct for 1H, and indirect for 13C and 15N). Actually I always have to look back and forth for referencing, so thought why not make a small script and put it on web so that the access becomes handy.

!!! The referencing should be done on the day of recording experiments !!!

!!! No rounding off of frequency numbers !!!

  1. Record a one-D (1H) spectrum (s2pul on Varian and zg on Bruker) of the buffer (or sample) containing DSS.
  2. Set the cursor on the right most line (DSS line) in the 1H spectrum of the sample. For Varian, type rl(0p) to set the DSS line to 0 ppm. In Bruker, use one of the buttons on the top panel to do the same.
  3. Type movetof (Varian) to set the tof at DSS line. In Bruker, use one of the buttons on the top panel to set the O1 at DSS line.
  4. Check the 1H frequency (spcfrq command in Varian will display four values, use the first one: RF Channel 1 (Obs) frequency). This frequency will be called as H0

Now,

  1. For proton refrencing, check for frequency numbers against sfrq (Varian) or SFO1 (Bruker) values in the procpar file (Varian) or the acqu file (Bruker) of any experiment; call them as Hval.
  2. For nitrogen refrencing, check for frequency numbers against dfrq2 (Varian) or SFO3 (Bruker) values in the procpar file (Varian) or the acqu file (Bruker) of any experiment; call them as Nval.
  3. For carbon-aliphatic refrencing, check for frequency numbers against dfrq (Varian) or SFO2 (Bruker) values in the procpar file (Varian) or the acqu file (Bruker) of any of the HNCA, CBCANH type experiment; call them as CAval.
  4. For carbonyl refrencing, check for frequency numbers against dfrq (Varian) or SFO2 (Bruker) values in the procpar file (Varian) or the acqu file (Bruker) of HNCO and HN(CA)CO type experiment; call them as COval.

References:

  1. Wishart et al, “1H, 13C and 15N chemical shift referencing in biomolecular NMR”, JBNMR (1995), 6, 135-140.
  2. Wishart et al, “Protein chemical shift analysis: a practical guide”, Biochem. Cell Biol. (1998), 76, 153-163.

How to increase the impact factor of Indian journals…???

Through this post I want to put forward a suggestion, in front of scientists in India, regarding how to increase the impact of Indian journals. I suggest that Indian Govt should make a rule, which should be applicable to all the universities and institutes across India, that we, the researchers of India should publish all the work in Indian Journals only. The journals may be peer-reviewed internationally. The journals may be available online free of cost, and free copies may be sent to major universities worldwide. The language used should be ‘english’ so that the fate should not be like Russians, who did this in russian language and their developments in science were restricted to themselves.
This would be a difficult thing specially when there is a tough “race” going among scientists to see their names in international journals of highest impact, however, this would certainly increase the level of recognition the Indian Scientists should get worldwide.
Well, initially students may face problems, as in the average impact factor per student will be certainly very low, however, as soon as the Indian work starts getting recognition, citations will increase and thus the impact factor. I have a strong feeling that this should work. The post is open for suggestions/discussion. I would appereciate visitors of this page for their comments.

visit to NMRS 2008

A great experience of the delhi-hospitality was exemplified by INMAS people in the NMRS 2008 meeting during 16-19 Jan 2008. Although there was a little confusion during first entry in the DRDO campus…but later on the meeting was memorized by good lectures, good food, and good location. NMRS 2009 was announced to be held in IICT, Hyderabad and NMRS 2010 in IISc, Bangalore.