[PyMOL] On creating and editing protein structures

2012-05-13 Thread John Ladasky
Hello everyone, I have two issues on which I would seek your advice. I am using PyMol 1.4.1. The first concerns creating protein structures from scratch. I select Build > Residue from the menu, and then I select my desired secondary structure. Then I use the Alt shortcut keys to add amino

[PyMOL] PyMol memory, disk, and CPU usage

2012-02-09 Thread John Ladasky
I'm currently using PyMol 1.4.1 on Ubuntu Linux 11.10.  My hardware is fairly up-to-date, an AMD 6-core, 3.2 GHz CPU ,and 4 GB of DDR1200 RAM.  My only old hardware is my NVidia 8800 GTS graphics card.  I have started to assemble rather large visualizations. I am noticing CPU performance lags, a

Re: [PyMOL] PyMol 1.4 not running on Ubuntu Linux 11.10

2012-01-11 Thread John Ladasky
From:Pete Meyer To: John Ladasky Cc: "pymol-users@lists.sourceforge.net" Sent: Wednesday, January 11, 2012 10:09 AM Subject: Re: [PyMOL] PyMol 1.4 not running on Ubuntu Linux 11.10 Hi John, > > >I don't think you need a re-install.  My take on the problem is that

[PyMOL] PyMol 1.4 not running on Ubuntu Linux 11.10

2012-01-10 Thread John Ladasky
Hi folks, I just upgraded my Ubuntu Linux installation to 11.10.  Of course, this removes obsolete versions of applications.  So I had to reinstall PyMol. The Ubuntu Linux 11.10 manifest states that PyMol 1.4.1 is the supported version, and a package file is available.  So, I downloaded and (su

[PyMOL] Forced Linux/Python upgrade, killed PyMol, please help!

2011-12-21 Thread John Ladasky
Hello everyone. It has been a while since I posted here. Apologies to the admins, I tried to subscribe again, and I forgot that I was already subscribed. For some non-PyMol work, I was obligated to upgrade my operating system to Ubuntu Linux 11.10. In fact, the specific reason that I had to

[PyMOL] [Solved] Upgraded computer, Pymol usable again. :^)

2009-10-23 Thread John Ladasky
Hello again,   With some hints from Ubuntu Forums, I tracked down and corrected my problem.  Hopefully this will be of help to someone else.   The fancy new desktop rendering schemes which are part of Ubuntu v.8, but which were not part of Ubuntu v.6, use 3D graphics to grow, shrink, and move wi

[PyMOL] Upgraded computer, PyMol now unusable :^(

2009-10-23 Thread John Ladasky
Hi folks,   I was using PyMol with no problems about a year ago.  I believe that my PyMol version was in the 0.9x series.  I was using Ubuntu Linux 6.06 on a Pentium IV machine.   Since then I have upgraded to a new multi-core motherboard, and Ubuntu Linux 8.04.  The Linux repository has a PyM