Hi Nicole, So, marking Warrens words, the question is, did anything else in your configuration change? Hardware, operating system, device drivers? That is a more likely cause for your problem. Otherwise, is the problem reproducible? Good behaviour with before version, bad behaviour with 'fixed' version of a pdb file. In that case, it would be most helpful if you could provide the two versions of a pdb file and a cookbook description (script) of what you're doing to run into the problem.
Cheers, Tsjerk On 9/5/07, DeLano Scientific <del...@delsci.info> wrote: > > > Nicole, > > 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. > > > Cheers, > Warren > > > ________________________________ > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On > Behalf Of Nicole Lewis-Rogers > Sent: Tuesday, September 04, 2007 3:28 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Problem with using Zoom command & difficulty > movingmolecules > > > > Hi, > > 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 > > ________________________________ > Need a vacation? Get great deals to amazing places on Yahoo! Travel. > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
