load many PDBs in your pymol

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.

PDBSum announces topology diagrams for protein domains

Like what you see above, it’s a protein topology diagram (sample: 1PJW.pdb). Starting on Feb Sixth, 2006, the PDBSum (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/)  announces the new service which provides the topology diagram of the coordinate file in Protein Data Bank (http://www.rcsb.org/pdb).

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.

Beginning Perl

http://learn.perl.org/library/beginning_perl/

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.

making dimer PSF

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
   stop
   (by JK)
2. In the Python interface, easiest is:
   seq=”’ string containing three character residue names”’import psfGen
   psfGen.seqToPSF(seq,segName=’A')
   psfGen.seqToPSF(seq,segName=’B')

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