My software notes

April 12, 2011

PyMOL-electrostaic surface view

Filed under: pymol/ molmol,softwares and scripts — kpwu @ 8:04 pm
Tags: , ,

To make electrostatic surface view of protein using PyMOL, two ways are often suggest. One option is using ABPS to generate the electrostatic map. Here is one nice instruction at PyMOLwiki using ABPS. Another option is using Delphi developed by Barry Honig group to generate the electrostatic map of protein.

I am writing a note at here using Delphi to generate electrostatic surface map of proteins in PyMOL as I learned from one online howto.

  1. download Delphi and uncompress it.
  2. edit the delphi.param.
    Basically, just need to replace the filename of the PDB you are going use.
  3. run “$PATH/delphi $PATH/delphi.param.
    The default name of output is fort.20 and I rename it to “xxx.phi”
  4. In PyMOL, load the protein first. Assume the object name of loaded protein is “new_protein”. Show the surface and remove all other shows (lines as default, or cartoon..)
  5. At PyMOL command terminal, type:
    load xxx.phi, emap
    (The emap object is then created).
  6. type: ramp_new elvl, emap, [-2,0,2] to create an object of the electrostatic level with a rang of -2 (red) to 0 (white) and to 2 (blue). The range can be changed. E.g. [-7, 0, 7].
  7. type: set surface_color, elvl, new_protein

Here is the example I have using my project protein:

Note:

  • I have tried Delphi on my iMac and on a Linux cluster. Although I used same delphi.param, delphi can’t successfully calculate the electrostatic map for me on iMac.
  • I saw people use ABPS+PyMOL to make electrostatic surface views for TWO proteins in ONE PyMOL window. I tried doing similar thing using the steps I noted at here, not successful to show two different electrostatic views for two proteins (I generated two maps separately).
Advertisements

1 Comment »

  1. […] to “Draw the electrostatic surface” can be checked at my earlier post, […]

    Pingback by [PyMOL] side-by-side comparison of 3 electrostatic surface potentials « My software notes — September 18, 2012 @ 2:22 am | Reply


RSS feed for comments on this post. TrackBack URI

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Create a free website or blog at WordPress.com.

%d bloggers like this: