Thomas and Martin I have tried both suggestions. Still it did not work out.
Regards
Abida

From: abida_siddiqa@hotmail.com
To: pymol-users@lists.sourceforge.net
Subject: Pymol visualization problem
Date: Tue, 8 Jan 2013 10:12:46 +0500

Hello, 

I have docked one protein named 'L1'( 450 amino acid) with another protein
named 'E2'(68 amino acid, Chain A) and used pymol-v1.3r1-edu-Win32.msi to visualize
the complex. my system is windows 7 , 64 bit. The problem is, i am unable
to see the sequence of 'E2' protein and so as its structure. In order to
confirm, if it is docking problem or visualization problem, i have used
swiss pdb viewer. it has shown me sequence and structure of both proteins. i
wonder why can not i see it in pymol.
secondly, i docked L1 and E2 ( this time used chain A and B of it), and
visualized the complex in pymol. i was only able to see L1, and chain A of
E2 (both chain A and B are alike). Then in order to see if it is docking
error or visualization error, i rendered the complex in swiss pdb viwer and
saw the L1 and E2 (both chain A and B).
Thirdly, i changed the docking software and generated a complex using
another software, this time i still was unable to visualize complete complex
in pymol.
Any help will be much appreciated.
Kind regards
Abida