Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-23 Thread Gilles Truan
:28 PM To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-23 Thread Gilles Truan
Message- From: Nathan Baker [mailto:nathanaba...@mac.com] Sent: Wednesday, September 17, 2008 6:28 PM To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-22 Thread Gilles Truan
@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm curious, though -- why would a PyMOL APBS invocation ever see the PDB file

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-22 Thread Yong Huang
-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm curious, though -- why would a PyMOL APBS invocation ever see the PDB file? Wouldn't a user first convert it to PQR with PDB2PQR

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-22 Thread Thomas Stout
: David Gohara; apbs-us...@lists.sourceforge.net list; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS Dear all, Sorry for the late answer but I finally managed to find what the error is... First thing, I work on a Windows XP environment (nobody's

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-18 Thread Gilles Truan
To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-18 Thread Nathan Baker
...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited. I'm curious, though -- why would a PyMOL APBS invocation ever see the PDB file? Wouldn't a user first convert

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-17 Thread Chris Swain
Hi, I noticed the latest version of the PDB file format description was posted today. http://www.wwpdb.org/docs.html Chris On 17 Sep 2008, at 20:21, DeLano Scientific wrote: The PyMOL and APBS programs have differing views as to whether PDB PQR files are column-based or

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-17 Thread Nathan Baker
Of Gilles Truan Sent: Wednesday, September 17, 2008 1:09 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Strange behaviour with APBS I have noticed a strange behaviour of the APBS module. I used it a lot recently and it works perfectly for 95% of the structures I analyzed. I usually fetch

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

2008-09-17 Thread DeLano Scientific
:28 PM To: DeLano Scientific Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net; apbs-us...@lists.sourceforge.net Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS Hi Warren -- The PQR format (which doesn't really have a standard) is basically just whitespace delimited