My software notes

May 19, 2006

sequence dependent random coil corrections

Filed under: softwares and scripts — kpwu @ 9:23 pm
Tags:

GOAL: make a script that takes sequence as an input and returns a sequence-dependent corrections of random coil chemical shifts of CA, CO, HN, N and HA.

References:

  1. Sequence-depent Correction of Random Coil NMR Chemical Shifts (JACS, 2001, 123, 2970-2978)
  2. Random coil chemical shifts in acidic 8M urea:Implementation of random coil shift data in NMRView (JBNMR, 2000, 18, 43-48)

Author Kuen-Phon Wu, Dept Chem, Rutgers University May 19th, 2006

Downloadable place at Ubuntu One (update 2011, 08-12)

snapshot of results of all HN,HA,CA,CB,CO and N

seq dept corrected random coil shifts

 

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17 Comments »

  1. Dear Sir,
    I am a phd student. I am veru much interested to get the scripts.
    I will be very obliged if you send me the scripts at shovanlal_gayen@yahoo.co.in.
    thanking you
    best regards
    shovanlal

    Comment by Shovanlal Gayen — February 27, 2007 @ 8:26 am | Reply

  2. Hi kpwu!
    Nice script you have there! I’m graduated in Chemistry and currently studying metalloproteins. I’m also interested in your scripts. I’ll be very grateful if you send it to me.

    Thank you.

    Comment by Iven — May 11, 2007 @ 2:22 am | Reply

  3. I am a Ph.D Student and right now doing protein NMR. I am interested in your script and it will be very helpful to me if you will send this script to me.
    Thanks

    Comment by Avay — June 15, 2007 @ 12:17 pm | Reply

  4. Will you please that version which i can run on windows Xp
    Thanks.

    Comment by Avay — June 16, 2007 @ 4:00 am | Reply

  5. Hi Avay,

    I guess that my script doesn’t work on windowsXP even if you install the UNIX tools on your windowsXP. If you can’t get a UNIX-based machine, you can send me your sequence and I will run the script for you.

    kpwu

    Comment by kpwu — June 16, 2007 @ 6:09 am | Reply

  6. O.k. fine. Thanks for your help.
    Please send the unix script. I’ll run it on Unix.

    Comment by Avay — June 16, 2007 @ 9:03 am | Reply

  7. Hi there,

    Could you please send me the script?

    Thnaks a lot!

    Ben

    Comment by Ben — September 19, 2007 @ 10:41 am | Reply

  8. Hi Ben,

    Now you can download the file via this blog.

    kpw, 9/19

    Comment by kpwu — September 19, 2007 @ 12:40 pm | Reply

  9. Hi KPW,

    How should the input file (one-letter sequence) look like?
    Does it need to have a special formatting?

    Thanks,

    Ben

    Comment by Ben — September 19, 2007 @ 9:27 pm | Reply

  10. Yes, one-letter-code sequence. The header also says the info:usage=”Usage: ./randomcoilshift.sh [one_letter_code_seq_file]”

    Comment by kpwu — September 20, 2007 @ 6:23 am | Reply

  11. I did use a file like that contains only the one letter code sequence.
    When I run the script, it calculates the chemical shift of the first residue R and then displays zero for the 2 following residues only.
    It also displays an error message stating that there is an error in reading lines ), -1, +1.

    Ben

    Comment by Ben — September 20, 2007 @ 7:48 am | Reply

  12. Hi Ben,

    Are you using Mac?
    I did a test on my Macbook pro (OS X) and got some errors like you said. Please download the special version for Mac users. I just upload and make the link.

    Comment by kpwu — September 20, 2007 @ 9:42 am | Reply

  13. Yes! I’m using MacOS X.
    Thanks for the new link.

    Ben

    Comment by Ben — September 20, 2007 @ 10:04 am | Reply

  14. hey,,

    gud work,, very very useful script, downloaded it.

    Comment by raghav — June 25, 2008 @ 6:52 am | Reply

  15. Hi,
    I would appreciate getting a copy of this script. I can’t seem to find a download link on the web page. Could you send it to me, or otherwise make it available?

    Thanks,
    David

    Comment by David — August 12, 2011 @ 5:38 pm | Reply

  16. Hi David,

    You can try the link “http://ubuntuone.com/p/1A0g/”. WordPress doesn’t allow me to share a “.sh” file. I put it at my Ubuntu One place. The link is also provided in the main text.

    The script should work well for Mac and Linux systems. Let me know if the script doesn’t work well in your system.

    Comment by kpwu — August 12, 2011 @ 6:26 pm | Reply

  17. Kuen-Phon,
    Thanks very much. We’ll give it a try.
    David

    Comment by David — August 17, 2011 @ 12:06 pm | Reply


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