My software notes

April 1, 2011

pynmr — an excellent PyMol’s NMR extension

Filed under: pymol/ molmol — kpwu @ 6:43 pm
Tags: ,

When I installed PyMol on my iMac using Fink, I found there are some plugins installed already. One of the famous plugin is PDB loader, I believe every one loves it a lot. A new one (at least it’s new to me) is NMR extension (pyNMR) written by a Canadian group. Thank you! I’m lovin it so much.

I don’t know if the downloaded PyMol for Linux or MS-Win also has this plugin installed. If you are an NMR user and want to use PyMol as the main molecular viewer, this is a must-have plugin.

When you click the “NMR Extension”, this pop up window is small as shown below:

At toolbar “File” provides ways to load either single or multiple PDBs as I always did in MOLMOL. Very convenient to load structures. Load PDBs by rootname and number range is another good thing I like a lot.

To load multiple PDBs in one time, simply make a list of taget PDB you want in the .nam file and load the file by clicking the “Load button”. You can see PDBs are loaded in your PyMol main window, like mine:

The structures are not superimposed well and we can do it using the pynmr extension.
Click special in the pynmr window and you will see a refreshed window like this:

I always check on the ” Display Backbone Only” to see backbone trace in the pymol window. If you don’t have a preferred range to do pairwise fit, just click “Do Fit” button and you can all molecules in PyMol window move to the best position. Users can also define the atoms to be superimposed. The plugin provides “C O N CA” and “C N CA” options by default.
You can also see the RMSD (average to mean structure) in the message window. I have checked very times using different calculated multiple structures (different proteins) between this pynmr plugin and MOLMOL, the calculated RMSD values are almost same. Differences happen at the second decimal. Here are the results:


You can also have your own define range in the “Residue range” option, e.g. 10-12,23-34,44-55.
THERE IS NO SPACE between the comma and numbers! Another option is use the “Fit” button to ask the program to guess the best range for you. Unlucky to me, I frequently got all PyMol crashed. Since I know what range/residues I want to use for superimpose, I always manually define the range.

Personally, I don’t like to see oxygen shown in this backbone trace. The default color scheme is too colorful to see the  trace. So I always make all molecules in gray (or gray30) and hide the backbone oxygens. The picture is much better as shown below:

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4 Comments »

  1. Hi, how to convert a list of PDB files to a single NAM file?

    Comment by Anh Hung MAI — November 7, 2011 @ 4:35 am | Reply

  2. If I am right, NAM is a list file used earlier in MOLMOL. You just need to generate a text file (called xx.nam) which has all the file names of your interested pdb files. In the NAM file, one line only contains one PDB file, that is, for 20 interested PDBs, you will have a 20-line NAM file.

    Comment by kpwu — November 7, 2011 @ 11:32 am | Reply

    • Yeap, you’re right. I’m using MOLMOL. I’m just a newbie on this kind of software ^^
      Thank you for your instruction!

      Comment by Anh Hung MAI — November 7, 2011 @ 12:16 pm | Reply

  3. Hi, I was wondering if you are still using this plunin. I downloaded the code form the link above, and it looks like there is some issue with compiling and that the Numeric Python (NumPy) version might be dated. I’m running PyMOL OpenSource 1.7x on Mac OS X 10.10.2. I know it’s not your software, but thought that maybe you were keeping up with it. Thanks for the great post. I look forward to getting this up and running. Best, Scott

    Comment by scott — February 20, 2015 @ 4:11 pm | Reply


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