Hi Abida
Is it possible that you have multiple states in your PDB file? Try
clicking the arrow in the bottom right corner of PyMOL and see if
you can display the other protein. If so, you probably need to delete
the MODEL and END from your PDB file. Then all should appear at once.
Martin
Hi Briony,
this sounds like a very cool project!
Regarding question 1: If your PDB DNA model is long enough, you can use
cafit_orientation from the psico module (a PyMOL extension) to draw
the axis. It determines the axis by least-square linear fit on the
backbone atoms. This requires a recent
Thomas and Martin I have tried both suggestions. Still it did not work
out.RegardsAbida
From: abida_sidd...@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
Hi Abida,
thanks for the PDB file that you sent me off-list.
It is a naming conflict, you have more than one chain A which have
overlapping residue numbers and even IDs. You can still load them like this:
PyMOL set retain_order
PyMOL load complex.1.pdb
PyMOL as cartoon
I also suggest to fix
I created a session file with Pymol Version 1.5.0.4 that I am unable to open up
on my laptop which is running 1.2r5pre. I am able to see the first state but
all of the other remaining states are lost. I haven't had opening session
files with saved states in the past so I do not suspect it is
The handling of density maps changed with (I believe) version 1.5 -
earlier versions would just load the map as given, later ones appear to
try to do symmetry expansion (even if the map isn't covering the ASU).
I've seen this result in a similar error message when loading session
files (with
Hi,
I have a model of DNA-Ligand, defualt both ligand and DNA are represented
as sticks i make DNA as cartoon and ligand as stick, this is general
presentation
DNA molecule has internal HBONDS too.. how can i see the hbonds made
between just ligand and DNA, ???
how can i show just
