It doesn’t matter to know who I am. I am currently a graduate student studying biophysics and biochemistry at Rutgers University, the state university of New Jersey at New Brunswick.
My main research tools are NMR and computers and my research targets are some natively unfolded proteins they are amyloid disease related. The goal is that I want to know or I want to make some connections between protein misfolding and protein aggregation.
My personal interests are protein chemistry and bioinformatics. That’s why I create this blog. There are so many commands of many software that I have to remember, however, it’s very difficult to keep them in my brain freshly. The main purpose creating this blog is to record several essential commands about nmrpipe, nmrview, sparky, molmol, pymol and some shell scritps I wrote.
Please feel free to give me comments. I am very happy to receive comments and have interactions with you.
Best wishes,
kpwu
Publications (links are provided in the “my current publications“):
- Structural basis of a flavivirus recognized by its neutralizing antibody: solution structure of the domain III of the Japanese encephalitis virus envelope protein.
J Biol Chem. 2003 Nov 14;278(46):46007-13. Epub 2003 Sep 2.
- Novel solution structure of porcine beta-microseminoprotein.
J Mol Biol. 2005 Mar 4;346(4):1071-82. Epub 2005 Jan 16. - 1H, 13C and 15N resonance assignments and secondary structure of murine angiogenin 4.
J Biomol NMR. 2005 Feb;31(2):175-6. - Distinguishing among Structural Ensembles of the GB1 Peptide: REMD Simulations and NMR Experiments.
J Am Chem Soc. 2007 Apr 3 - Characterization of conformational and dynamic properties of natively unfolded human and mouse alpha-synuclein ensembles by NMR: implication for aggregation.
J Mol Biol. 2008 May 16;378(5):1104-15. Epub 2008 Mar 18.
Determined Protein Structure:
Solution Structure of the Domain III of the Japan Encephalitis Virus Envelope Protein, PDB code: 1PJW
BMRB Entries:
- 5565: Backbone 1H, 13C, and 15N Chemical Shift Assignments for porcine MSP
- 6279: 1H, 13C and 15N resonance assignments and secondary structure of the murine angiogenin 4
- NMR Restraints of 1PJW at BMRB
Hi,
I’m trying to modify your script cal-HH-distance.sh to calculate
atom-atom distances in a PDB,
such as O in H2O to OG1 in GLU.
Have you ever generalized your
script for such calculations ?
Best regards, Mike
Comment by Mike — September 18, 2007 @ 3:06 am |
Hi Mike,
I didn’t work for such purpose but it seems doable. I guess you want to calculate some H-bond/hydration by H2O. If there are too many H2O, the script I made won’t work well. I am not good in making scripts, so the efficiency isn’t high…
You may try MOLMOL or other programs first.
Comment by kpwu — September 18, 2007 @ 6:38 am |
hi there. could you please tell me how to change the dashed line to solid line (and set line width) in pymol using ‘dist’ function? my purpose is to draw a solid line between 2 atoms which i am interested. thanks.
———-
in the past, pyMOL users can only use “dist” command to make dash lines first, and changed the intervals of dash lines as “zero” to make a fake stick lines.
Comment by timic — November 28, 2007 @ 9:45 pm |
Hi,
It’s simple. Steps are shown:
1. dist “name” selected_atom1, selected_atom2
2. set dash_gap,0
Then the dash line will have “zero” gap, means “no” dashed at all.
Comment by kpwu — November 28, 2007 @ 11:15 pm |
hi there,
Found your blog by chance. I’ve put up a website nmrwiki.org – you can probably get the idea from the url.
You’re very welcome to join!
Cheers.
Evgeny. efadeev uci edu
Comment by Evgeny — February 6, 2008 @ 9:59 am |
Hi Evgeny,
Thanks for invitation. I am glad you make a great website. I am currently too busy to keep updating new stuff in this blog. Let’s see if I can have any contributions later.
My next plan is a short tutorial of Sparky. That is ~30-50 (word) pages in my plan talking about 2D data (fitting, overlay, …) and 3D data (assignment strategies)…
kpwu
Comment by kpwu — February 7, 2008 @ 5:10 pm |
Great, there are already some sparky tutorials on the wiki and a couple of custom scripts there too.
I’ll be moving towards setting up wiki on a dedicated server and adding more managers so we can have a truly community-built resource.
Will let you know when that happens.
Cheers.
Evgeny.
Comment by Evgeny — April 3, 2008 @ 8:40 am |
Hi kpwu,
I found your blog accidentally, but it’s just great. I’m also a graduate student in Rutgers, my lab is mainly a NMR lab at CABM, and my main focus is bioinformatics also. But I am really just a beginner in Biophysics and NMR. Hope I can learn a lot from your blog.
Best,
Smellycat
Comment by Smellycat — August 8, 2008 @ 7:24 am |
Hello,
I was wondering if anyone has a script that does the following: Given a .tbl list of NOEs, finds entries with ambiguous assignments and copies the higher NOE distance to both entries. This would be really helpful due to the highly complicated nature of this problem.
Thanks in advance
Comment by Nik — August 26, 2008 @ 12:50 pm |
Hi kpwu,
Want to let you know that NMR Wiki is looking for hardened
hackers to push the project to the limit.
You’re very welcome to join us!
Kind regards,
Evgeny.
Comment by Evgeny — March 12, 2009 @ 9:10 am |
Hi, my name andry, i’m interest too in bioinformatics field, but my background study is biochemistry..and now i’m one of the bioinformatics staff in Eijkman Institute for Molecular Biology in Indonesia..nice to know you!..i want to ask you, how to create ramachandran plot using PyMOL..?thanks before.
Comment by andrykidd — November 29, 2009 @ 8:10 pm |