From: Karl O. <obe...@me...> - 2008-02-28 17:07:24
|
Hi All, Up until about a month ago I successfully made surfaces from jvxl files that I copied from the console using the show command. Since that time the surfaces generated from the jvxl files are not the same as the original computed surface. The jvxl files made before that time still generate the correct surface. The link below contains two examples. http://www.messiah.edu/departments/chemistry/molscilab/jtat_080120/acetylcholinesterase/testing/chapter.htm Karl |
From: Bob H. <ha...@st...> - 2008-02-28 17:42:23
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Karl, I will look into this. Can you send me two JVXL files -- one old and one new -- and the script you used to generate them? Bob Karl Oberholser wrote: > Hi All, > Up until about a month ago I successfully made surfaces from jvxl > files that I copied from the console using the show command. Since > that time the surfaces generated from the jvxl files are not the same > as the original computed surface. The jvxl files made before that > time still generate the correct surface. The link below contains two > examples. > > http://www.messiah.edu/departments/chemistry/molscilab/jtat_080120/acetylcholinesterase/testing/chapter.htm > > Karl > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Bob H. <ha...@st...> - 2008-02-29 11:10:03
|
Bug fixed. I'm not convinced that WRITE ISOSURFACE has ever written correct files for isosurfaces created using the MINSET or POCKET options. By the way, Karl, I recommend NOT including the "sasurface" keyword in your isosurface pocket command, or if you do, use "sasurface 0". When you use sasurface just by itself it adds 1.2 Angstroms to the Van der Waals radius. That's fine for an overall approximation of the molecular surface, but it doesn't really give (in my opinion) the appropriate sense of how large a cavity is. The real cavity size is better represented by the Van der Waals surface, I think. Bob Karl Oberholser wrote: > Hi All, > Up until about a month ago I successfully made surfaces from jvxl > files that I copied from the console using the show command. Since > that time the surfaces generated from the jvxl files are not the same > as the original computed surface. The jvxl files made before that > time still generate the correct surface. The link below contains two > examples. > > http://www.messiah.edu/departments/chemistry/molscilab/jtat_080120/acetylcholinesterase/testing/chapter.htm > > Karl > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |
From: Karl O. <obe...@me...> - 2008-03-11 15:37:43
|
>>>> Bob Hanson <ha...@st...> 2/29/2008 6:09 AM >>> >By the way, Karl, I recommend NOT including the "sasurface" keyword in >your isosurface pocket command, or if you do, use "sasurface 0". When >you use sasurface just by itself it adds 1.2 Angstroms to the Van der >Waals radius. That's fine for an overall approximation of the molecular >surface, but it doesn't really give (in my opinion) the appropriate >sense of how large a cavity is. The real cavity size is better >represented by the Van der Waals surface, I think. > >Bob > If I use cavity rather than sasurface as the keyword I obtain more realistic looking cavities. For clarity of my own thinking, does cavity give a Van der Waals surface? Karl >Karl Oberholser wrote: > >> Hi All, >> Up until about a month ago I successfully made surfaces from jvxl >> files that I copied from the console using the show command. Since >> that time the surfaces generated from the jvxl files are not the same >> as the original computed surface. The jvxl files made before that >> time still generate the correct surface. The link below contains two >> examples. >> >> http://www.messiah.edu/departments/chemistry/molscilab/jtat_ >080120/acetylcholinesterase/testing/chapter.htm >> >> Karl >> >> >>------------------------------------------------------------------------ >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by: Microsoft >>Defy all challenges. Microsoft(R) Visual Studio 2008. >>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >>------------------------------------------------------------------------ >> >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >-- >Robert M. Hanson >Professor of Chemistry >St. Olaf College >Northfield, MN >http://www.stolaf.edu/people/hansonr > > >If nature does not answer first what we want, >it is better to take what answer we get. > >-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: Bob H. <ha...@st...> - 2008-03-11 17:05:52
|
Karl Oberholser wrote: >>>>>Bob Hanson <ha...@st...> 2/29/2008 6:09 AM >>> >>>>> >>>>> >>By the way, Karl, I recommend NOT including the "sasurface" keyword in >>your isosurface pocket command, or if you do, use "sasurface 0". When >>you use sasurface just by itself it adds 1.2 Angstroms to the Van der >>Waals radius. That's fine for an overall approximation of the molecular >>surface, but it doesn't really give (in my opinion) the appropriate >>sense of how large a cavity is. The real cavity size is better >>represented by the Van der Waals surface, I think. >> >>Bob >> >> >> > >If I use cavity rather than sasurface as the keyword I obtain more >realistic looking cavities. For clarity of my own thinking, does cavity >give a Van der Waals surface? > > Yes, I think it defaults to that. >Karl > > > > >>Karl Oberholser wrote: >> >> >> >>>Hi All, >>>Up until about a month ago I successfully made surfaces from jvxl >>>files that I copied from the console using the show command. Since >>>that time the surfaces generated from the jvxl files are not the same >>>as the original computed surface. The jvxl files made before that >>>time still generate the correct surface. The link below contains two >>>examples. >>> >>>http://www.messiah.edu/departments/chemistry/molscilab/jtat_ >>> >>> >>080120/acetylcholinesterase/testing/chapter.htm >> >> >>> >>>Karl >>> >>> >>>------------------------------------------------------------------------ >>> >>>------------------------------------------------------------------------- >>>This SF.net email is sponsored by: Microsoft >>>Defy all challenges. Microsoft(R) Visual Studio 2008. >>>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> >>>------------------------------------------------------------------------ >>> >>>_______________________________________________ >>>Jmol-users mailing list >>>Jmo...@li... >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>-- >>Robert M. Hanson >>Professor of Chemistry >>St. Olaf College >>Northfield, MN >>http://www.stolaf.edu/people/hansonr >> >> >>If nature does not answer first what we want, >>it is better to take what answer we get. >> >>-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >>------------------------------------------------------------------------- >>This SF.net email is sponsored by: Microsoft >>Defy all challenges. Microsoft(R) Visual Studio 2008. >>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |