As much as we may enjoy blaming the PDB for the various shortcomings of their files, I cannot imagine how the changes they implemented could be causing the behaviors you describe.  Rather, it sounds to me like you may be having problems with either PyMOL itself, or the underlying OpenGL graphics drivers.

From: [] On Behalf Of Nicole Lewis-Rogers
Sent: Tuesday, September 04, 2007 3:28 PM
Subject: [PyMOL] Problem with using Zoom command & difficulty movingmolecules

I have been using PyMOL for quite some time with no problems, until I down loaded images from RCSB Protein Data Bank that have been "fixed."  These new versions of the same images I have been working with since December 2007 are difficult to manipulate in PyMOL.  For example, I used to be able to highlight an amino acid residue, left click, choose Orient, and the residue of interest would come into close focus.  Now with the revamped images from RCSB, when I use the Orient command the whole molecule shifts slightly, but the highlighted residue doesn't come into close focus and the zoom command does not work at all.  Also, I used to be able to move molecules around smoothly so that I could view all angles of a residue.  Now the molecule jumps around the screen.  When I'm trying to see which residues have polar contacts with the one of interest I can only look at the molecule from 1 or 2 different angles and generally this is not good enough to see which residues are bonded to which.
Has anyone experienced this or know how to problem solve this issue?
Thank you for your time,
Nicole Lewis-Rogers

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