My software notes

February 15, 2006

load many PDBs in your pymol

Filed under: pymol/ molmol — kpwu @ 10:07 pm

There are 12 prion protein structures, 12 PDBs otained from RCSB-PDB, you can use the pdb loader which is a plugin of pymol, don’t need to fetch the file at RCSB website.

And change your mouse mode from “viewing” to “editing” by click the right bottom region of your pymol, then you could use the middle button of your mouse to move individual structure to specfic location, making arrays.

Finally,apply cartoon, fancy helices, highlight color and rainbow color to each structure, and type “ray” to generated shadows, png xxx.png to output your files.

February 14, 2006

PDBSum announces topology diagrams for protein domains

Filed under: servers — kpwu @ 9:28 pm

NOTE (Nov.4th, 2011): I have made a new post showing how to generat such topology figure using online service provided by PDBSum.

Please click this post “[web server] protein structural¬†analysis” to read new post.



Like what you see above, it’s a protein topology diagram (sample: 1PJW.pdb). Starting on Feb Sixth, 2006, the PDBSum (¬† announces the new service which provides the topology diagram of the coordinate file in Protein Data Bank (

PDBsum intergrated many programs such as Procheck, WhatIF, Rasmol script and others. I really like the topology diagram generated by PDBSum, though I can’t find the source code from there. Hope they will release the source codes or compiled files for people who want to generate the topology diagrams of their fresh, before-submitting PDBs.

February 4, 2006

Beginning Perl

Filed under: softwares and scripts — kpwu @ 6:52 am

from the above URL, the online ebook (also PDF available) was written by Simon Cozens, I have read the first three chapters, and feel his expressions about the basic perl programming are very clear. I’d like to recommend people who don’t want to buy any printed books but want to learn perl, try the online documents, it’s a better choice.

Enjoying PERL.

February 3, 2006

making dimer PSF

Filed under: xplor/xplor-nih/cns — kpwu @ 10:34 pm

got from xplor-NIH discussion mailing list.

two ways to generate dimer PSF:

  1. If you have a PSF file for the monomer, it’s easy to create one for
    the dimer using the “classic”
    xplor interface. Try this:
    struct @monomer.psf end
    vector do (segid = “A”) (all)
    struct @monomer.psf end
    vector do (segid = “B”) (not segid A)
    write struct output = “dimer.psf” end
    (by JK)
  2. In the Python interface, easiest is:
    seq=”’ string containing three character residue names”’import psfGen

    #if you wish to save psf info:
    xplor.command(“write psf output=new.psf end”)
    (by CS)

Blog at