From: Robert H. <ha...@st...> - 2012-05-20 19:23:13
|
Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't realized that since I see the bounce reports anyway, anyone can send me large files by this list!) On Sun, May 20, 2012 at 1:57 PM, < jmo...@li...> wrote: > > > ---------- Forwarded message ---------- > From: Andrew Long <and...@gm...> > To: jmo...@li... > Cc: > Date: Sat, 19 May 2012 17:16:35 -0300 > Subject: Re: [Jmol-developers] possible isosurface bug > in these cases I used... > > load methylisocyanate.mol2 //or whatever file > isosurface molecular > dots > > > > On Fri, May 18, 2012 at 6:13 PM, Robert Hanson <ha...@st...> wrote: > >> looks to me like you didn't select the sulfur atom. In one case you may >> have used the IGNORE keyword and in the other case not. >> >> Please package those up as .jmol files and send them to me. >> >> write tobob.jmol >> >> Bob >> >> On Fri, May 18, 2012 at 3:24 PM, Andrew Long <and...@gm...>wrote: >> >>> while messing around with isosurfaces I ran into another possible bug. >>> >>> http://imgur.com/FO8x0 >>> >>> http://imgur.com/GR0tE >>> >>> I tried just thiocyanate and it seems to work. I've attached the mol2 >>> files. Where exactly in the code is the isosurfaces calculated? >>> >>> Cheers Andrew >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: A. H. <ang...@ua...> - 2012-05-20 19:42:51
|
I forwarded it from the admin control page. The message was stopped there due to its large attachment On 20 May 2012 at 14:23, Robert Hanson wrote: > > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't realized that since I see the > bounce reports anyway, anyone can send me large files by this list!) |
From: Robert H. <ha...@st...> - 2012-05-20 20:16:32
|
ah -- it's not magic! Thanks, Angel... On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...> wrote: > I forwarded it from the admin control page. The message was stopped there > due to its large > attachment > > > On 20 May 2012 at 14:23, Robert Hanson wrote: > > > > > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't > realized that since I see the > > bounce reports anyway, anyone can send me large files by this list!) > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Andrew L. <and...@gm...> - 2012-05-20 20:34:31
|
Awesome Thanks again. The exact commands i used was..... load *filename.mol2* isosurface molecular dots //for comparison. The dots command seems to lay out the surface perfectly but the isosurface command seems to have issues with the linear hetero atoms. I recreated this in the stock binary version. 12.2.22. and just to check in with my isosurface project and I've managed to produce some rather excellent pictures from it. http://imgur.com/zbcFi this is ~800 data points upscaled to 6200 vertexs using a radial weighted average using a gaussian function as the weighting function. On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...> wrote: > ah -- it's not magic! Thanks, Angel... > > > On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: > >> I forwarded it from the admin control page. The message was stopped there >> due to its large >> attachment >> >> >> On 20 May 2012 at 14:23, Robert Hanson wrote: >> >> > >> > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't >> realized that since I see the >> > bounce reports anyway, anyone can send me large files by this list!) >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Andrew L. <and...@gm...> - 2012-05-20 20:37:57
|
here's one more with the molecule visible. http://imgur.com/yLwug On Sun, May 20, 2012 at 5:34 PM, Andrew Long <and...@gm...>wrote: > Awesome Thanks again. The exact commands i used was..... > > load *filename.mol2* > isosurface molecular > dots //for comparison. > > The dots command seems to lay out the surface perfectly but the isosurface > command seems to have issues with the linear hetero atoms. I recreated > this in the stock binary version. 12.2.22. > > and just to check in with my isosurface project and I've managed to > produce some rather excellent pictures from it. > > http://imgur.com/zbcFi > > this is ~800 data points upscaled to 6200 vertexs using a radial weighted > average using a gaussian function as the weighting function. > > On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...> wrote: > >> ah -- it's not magic! Thanks, Angel... >> >> >> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >> >>> I forwarded it from the admin control page. The message was stopped >>> there due to its large >>> attachment >>> >>> >>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>> >>> > >>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't >>> realized that since I see the >>> > bounce reports anyway, anyone can send me large files by this list!) >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > |
From: Robert H. <ha...@st...> - 2012-05-20 20:46:27
|
so start over with me. I didn't do any fix there. I just read the file. So let's just do this again. load methylisocyanate.mol2 isosurface molecular that by itself gives you a fragmented surface? Bob On Sun, May 20, 2012 at 3:34 PM, Andrew Long <and...@gm...>wrote: > Awesome Thanks again. The exact commands i used was..... > > load *filename.mol2* > isosurface molecular > dots //for comparison. > > The dots command seems to lay out the surface perfectly but the isosurface > command seems to have issues with the linear hetero atoms. I recreated > this in the stock binary version. 12.2.22. > > and just to check in with my isosurface project and I've managed to > produce some rather excellent pictures from it. > > http://imgur.com/zbcFi > > this is ~800 data points upscaled to 6200 vertexs using a radial weighted > average using a gaussian function as the weighting function. > > On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...> wrote: > >> ah -- it's not magic! Thanks, Angel... >> >> >> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >> >>> I forwarded it from the admin control page. The message was stopped >>> there due to its large >>> attachment >>> >>> >>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>> >>> > >>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't >>> realized that since I see the >>> > bounce reports anyway, anyone can send me large files by this list!) >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Andrew L. <and...@gm...> - 2012-05-20 20:49:21
|
yep is that not happening with you?(i haven't added in your recent patch) On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...> wrote: > so start over with me. I didn't do any fix there. I just read the file. So > let's just do this again. > > load methylisocyanate.mol2 > isosurface molecular > > that by itself gives you a fragmented surface? > > Bob > > > On Sun, May 20, 2012 at 3:34 PM, Andrew Long <and...@gm...>wrote: > >> Awesome Thanks again. The exact commands i used was..... >> >> load *filename.mol2* >> isosurface molecular >> dots //for comparison. >> >> The dots command seems to lay out the surface perfectly but the >> isosurface command seems to have issues with the linear hetero atoms. I >> recreated this in the stock binary version. 12.2.22. >> >> and just to check in with my isosurface project and I've managed to >> produce some rather excellent pictures from it. >> >> http://imgur.com/zbcFi >> >> this is ~800 data points upscaled to 6200 vertexs using a radial weighted >> average using a gaussian function as the weighting function. >> >> On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...>wrote: >> >>> ah -- it's not magic! Thanks, Angel... >>> >>> >>> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >>> >>>> I forwarded it from the admin control page. The message was stopped >>>> there due to its large >>>> attachment >>>> >>>> >>>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>>> >>>> > >>>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't >>>> realized that since I see the >>>> > bounce reports anyway, anyone can send me large files by this list!) >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Bob H. <ha...@st...> - 2012-05-20 22:58:19
|
Are you doing this in eclipse? Or using Jmol.jar? Are you doing the compiling? Maybe you are not getting clean compiling. Please try it at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can just drag drop files into that. Sent from my stupid iphone On May 20, 2012, at 3:52 PM, Andrew Long <and...@gm...> wrote: > I've attached the azide that also seems to cause this with just the isosurface molecular. > > On Sun, May 20, 2012 at 5:49 PM, Andrew Long <and...@gm...> wrote: > yep is that not happening with you?(i haven't added in your recent patch) > > > On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...> wrote: > so start over with me. I didn't do any fix there. I just read the file. So let's just do this again. > > load methylisocyanate.mol2 > isosurface molecular > > that by itself gives you a fragmented surface? > > Bob > > > On Sun, May 20, 2012 at 3:34 PM, Andrew Long <and...@gm...> wrote: > Awesome Thanks again. The exact commands i used was..... > > load filename.mol2 > isosurface molecular > dots //for comparison. > > The dots command seems to lay out the surface perfectly but the isosurface command seems to have issues with the linear hetero atoms. I recreated this in the stock binary version. 12.2.22. > > and just to check in with my isosurface project and I've managed to produce some rather excellent pictures from it. > > http://imgur.com/zbcFi > > this is ~800 data points upscaled to 6200 vertexs using a radial weighted average using a gaussian function as the weighting function. > > On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...> wrote: > ah -- it's not magic! Thanks, Angel... > > > On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...> wrote: > I forwarded it from the admin control page. The message was stopped there due to its large > attachment > > > On 20 May 2012 at 14:23, Robert Hanson wrote: > > > > > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't realized that since I see the > > bounce reports anyway, anyone can send me large files by this list!) > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > <methylazide.mol2> > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers |
From: Andrew L. <and...@gm...> - 2012-05-20 23:54:03
|
hrmmmm strange. The online version is working just fine but it doesn't seem to want to work from my stock .jar that I have(i DLed the binary version to be sure) in addition to not working on the version I'm compiling through eclipse. I tried clearing Java's cache but that doesn't seem to work...... is there any cache in eclipse that has to be purged? On Sun, May 20, 2012 at 7:29 PM, Bob Hanson <ha...@st...> wrote: > Are you doing this in eclipse? Or using Jmol.jar? Are you doing the > compiling? Maybe you are not getting clean compiling. Please try it at > http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can > just drag drop files into that. > > Sent from my stupid iphone > > On May 20, 2012, at 3:52 PM, Andrew Long <and...@gm...> > wrote: > > I've attached the azide that also seems to cause this with just the > isosurface molecular. > > On Sun, May 20, 2012 at 5:49 PM, Andrew Long <and...@gm...>wrote: > >> yep is that not happening with you?(i haven't added in your recent patch) >> >> >> On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...>wrote: >> >>> so start over with me. I didn't do any fix there. I just read the file. >>> So let's just do this again. >>> >>> load methylisocyanate.mol2 >>> isosurface molecular >>> >>> that by itself gives you a fragmented surface? >>> >>> Bob >>> >>> >>> On Sun, May 20, 2012 at 3:34 PM, Andrew Long <and...@gm... >>> > wrote: >>> >>>> Awesome Thanks again. The exact commands i used was..... >>>> >>>> load *filename.mol2* >>>> isosurface molecular >>>> dots //for comparison. >>>> >>>> The dots command seems to lay out the surface perfectly but the >>>> isosurface command seems to have issues with the linear hetero atoms. I >>>> recreated this in the stock binary version. 12.2.22. >>>> >>>> and just to check in with my isosurface project and I've managed to >>>> produce some rather excellent pictures from it. >>>> >>>> http://imgur.com/zbcFi >>>> >>>> this is ~800 data points upscaled to 6200 vertexs using a radial >>>> weighted average using a gaussian function as the weighting function. >>>> >>>> On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...>wrote: >>>> >>>>> ah -- it's not magic! Thanks, Angel... >>>>> >>>>> >>>>> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >>>>> >>>>>> I forwarded it from the admin control page. The message was stopped >>>>>> there due to its large >>>>>> attachment >>>>>> >>>>>> >>>>>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>>>>> >>>>>> > >>>>>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I >>>>>> hadn't realized that since I see the >>>>>> > bounce reports anyway, anyone can send me large files by this list!) >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Live Security Virtual Conference >>>>>> Exclusive live event will cover all the ways today's security and >>>>>> threat landscape has changed and how IT managers can respond. >>>>>> Discussions >>>>>> will include endpoint security, mobile security and the latest in >>>>>> malware >>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>> _______________________________________________ >>>>>> Jmol-developers mailing list >>>>>> Jmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Robert M. Hanson >>>>> Professor of Chemistry >>>>> St. Olaf College >>>>> 1520 St. Olaf Ave. >>>>> Northfield, MN 55057 >>>>> http://www.stolaf.edu/people/hansonr >>>>> phone: 507-786-3107 >>>>> >>>>> >>>>> 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 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. >>>>> Discussions >>>>> will include endpoint security, mobile security and the latest in >>>>> malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Jmol-developers mailing list >>>>> Jmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>> >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> > <methylazide.mol2> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > |
From: Robert H. <ha...@st...> - 2012-05-21 03:43:41
|
Well, that's a relief to me but no solution for you. Make sure in Eclipse that you use from the top menu Project...Clean -- then build. On Sun, May 20, 2012 at 6:53 PM, Andrew Long <and...@gm...>wrote: > hrmmmm strange. The online version is working just fine but it doesn't > seem to want to work from my stock .jar that I have(i DLed the binary > version to be sure) in addition to not working on the version I'm compiling > through eclipse. I tried clearing Java's cache but that doesn't seem to > work...... is there any cache in eclipse that has to be purged? > > > On Sun, May 20, 2012 at 7:29 PM, Bob Hanson <ha...@st...> wrote: > >> Are you doing this in eclipse? Or using Jmol.jar? Are you doing the >> compiling? Maybe you are not getting clean compiling. Please try it at >> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can >> just drag drop files into that. >> >> Sent from my stupid iphone >> >> On May 20, 2012, at 3:52 PM, Andrew Long <and...@gm...> >> wrote: >> >> I've attached the azide that also seems to cause this with just the >> isosurface molecular. >> >> On Sun, May 20, 2012 at 5:49 PM, Andrew Long <and...@gm...>wrote: >> >>> yep is that not happening with you?(i haven't added in your recent patch) >>> >>> >>> On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...>wrote: >>> >>>> so start over with me. I didn't do any fix there. I just read the file. >>>> So let's just do this again. >>>> >>>> load methylisocyanate.mol2 >>>> isosurface molecular >>>> >>>> that by itself gives you a fragmented surface? >>>> >>>> Bob >>>> >>>> >>>> On Sun, May 20, 2012 at 3:34 PM, Andrew Long < >>>> and...@gm...> wrote: >>>> >>>>> Awesome Thanks again. The exact commands i used was..... >>>>> >>>>> load *filename.mol2* >>>>> isosurface molecular >>>>> dots //for comparison. >>>>> >>>>> The dots command seems to lay out the surface perfectly but the >>>>> isosurface command seems to have issues with the linear hetero atoms. I >>>>> recreated this in the stock binary version. 12.2.22. >>>>> >>>>> and just to check in with my isosurface project and I've managed to >>>>> produce some rather excellent pictures from it. >>>>> >>>>> http://imgur.com/zbcFi >>>>> >>>>> this is ~800 data points upscaled to 6200 vertexs using a radial >>>>> weighted average using a gaussian function as the weighting function. >>>>> >>>>> On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...>wrote: >>>>> >>>>>> ah -- it's not magic! Thanks, Angel... >>>>>> >>>>>> >>>>>> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >>>>>> >>>>>>> I forwarded it from the admin control page. The message was stopped >>>>>>> there due to its large >>>>>>> attachment >>>>>>> >>>>>>> >>>>>>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>>>>>> >>>>>>> > >>>>>>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I >>>>>>> hadn't realized that since I see the >>>>>>> > bounce reports anyway, anyone can send me large files by this >>>>>>> list!) >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Live Security Virtual Conference >>>>>>> Exclusive live event will cover all the ways today's security and >>>>>>> threat landscape has changed and how IT managers can respond. >>>>>>> Discussions >>>>>>> will include endpoint security, mobile security and the latest in >>>>>>> malware >>>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>>> _______________________________________________ >>>>>>> Jmol-developers mailing list >>>>>>> Jmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Robert M. Hanson >>>>>> Professor of Chemistry >>>>>> St. Olaf College >>>>>> 1520 St. Olaf Ave. >>>>>> Northfield, MN 55057 >>>>>> http://www.stolaf.edu/people/hansonr >>>>>> phone: 507-786-3107 >>>>>> >>>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Live Security Virtual Conference >>>>>> Exclusive live event will cover all the ways today's security and >>>>>> threat landscape has changed and how IT managers can respond. >>>>>> Discussions >>>>>> will include endpoint security, mobile security and the latest in >>>>>> malware >>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>> _______________________________________________ >>>>>> Jmol-developers mailing list >>>>>> Jmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>> >>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. >>>>> Discussions >>>>> will include endpoint security, mobile security and the latest in >>>>> malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Jmol-developers mailing list >>>>> Jmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>> >>>>> >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Professor of Chemistry >>>> St. Olaf College >>>> 1520 St. Olaf Ave. >>>> Northfield, MN 55057 >>>> http://www.stolaf.edu/people/hansonr >>>> phone: 507-786-3107 >>>> >>>> >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>> >> <methylazide.mol2> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Andrew L. <and...@gm...> - 2012-05-21 03:46:34
|
After much hair pulling I've narrowed it down to the fact that I had the 12.2.24 rather than the 12.2.25. Thanks again for the help narrowing this down. I'm going to Dif the code to figure out what went wrong. http://imgur.com/yQD79 Cheers Andrew On Sun, May 20, 2012 at 8:53 PM, Andrew Long <and...@gm...>wrote: > hrmmmm strange. The online version is working just fine but it doesn't > seem to want to work from my stock .jar that I have(i DLed the binary > version to be sure) in addition to not working on the version I'm compiling > through eclipse. I tried clearing Java's cache but that doesn't seem to > work...... is there any cache in eclipse that has to be purged? > > > On Sun, May 20, 2012 at 7:29 PM, Bob Hanson <ha...@st...> wrote: > >> Are you doing this in eclipse? Or using Jmol.jar? Are you doing the >> compiling? Maybe you are not getting clean compiling. Please try it at >> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can >> just drag drop files into that. >> >> Sent from my stupid iphone >> >> On May 20, 2012, at 3:52 PM, Andrew Long <and...@gm...> >> wrote: >> >> I've attached the azide that also seems to cause this with just the >> isosurface molecular. >> >> On Sun, May 20, 2012 at 5:49 PM, Andrew Long <and...@gm...>wrote: >> >>> yep is that not happening with you?(i haven't added in your recent patch) >>> >>> >>> On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...>wrote: >>> >>>> so start over with me. I didn't do any fix there. I just read the file. >>>> So let's just do this again. >>>> >>>> load methylisocyanate.mol2 >>>> isosurface molecular >>>> >>>> that by itself gives you a fragmented surface? >>>> >>>> Bob >>>> >>>> >>>> On Sun, May 20, 2012 at 3:34 PM, Andrew Long < >>>> and...@gm...> wrote: >>>> >>>>> Awesome Thanks again. The exact commands i used was..... >>>>> >>>>> load *filename.mol2* >>>>> isosurface molecular >>>>> dots //for comparison. >>>>> >>>>> The dots command seems to lay out the surface perfectly but the >>>>> isosurface command seems to have issues with the linear hetero atoms. I >>>>> recreated this in the stock binary version. 12.2.22. >>>>> >>>>> and just to check in with my isosurface project and I've managed to >>>>> produce some rather excellent pictures from it. >>>>> >>>>> http://imgur.com/zbcFi >>>>> >>>>> this is ~800 data points upscaled to 6200 vertexs using a radial >>>>> weighted average using a gaussian function as the weighting function. >>>>> >>>>> On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...>wrote: >>>>> >>>>>> ah -- it's not magic! Thanks, Angel... >>>>>> >>>>>> >>>>>> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua...>wrote: >>>>>> >>>>>>> I forwarded it from the admin control page. The message was stopped >>>>>>> there due to its large >>>>>>> attachment >>>>>>> >>>>>>> >>>>>>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>>>>>> >>>>>>> > >>>>>>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I >>>>>>> hadn't realized that since I see the >>>>>>> > bounce reports anyway, anyone can send me large files by this >>>>>>> list!) >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Live Security Virtual Conference >>>>>>> Exclusive live event will cover all the ways today's security and >>>>>>> threat landscape has changed and how IT managers can respond. >>>>>>> Discussions >>>>>>> will include endpoint security, mobile security and the latest in >>>>>>> malware >>>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>>> _______________________________________________ >>>>>>> Jmol-developers mailing list >>>>>>> Jmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Robert M. Hanson >>>>>> Professor of Chemistry >>>>>> St. Olaf College >>>>>> 1520 St. Olaf Ave. >>>>>> Northfield, MN 55057 >>>>>> http://www.stolaf.edu/people/hansonr >>>>>> phone: 507-786-3107 >>>>>> >>>>>> >>>>>> 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 >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Live Security Virtual Conference >>>>>> Exclusive live event will cover all the ways today's security and >>>>>> threat landscape has changed and how IT managers can respond. >>>>>> Discussions >>>>>> will include endpoint security, mobile security and the latest in >>>>>> malware >>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>> _______________________________________________ >>>>>> Jmol-developers mailing list >>>>>> Jmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>> >>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. >>>>> Discussions >>>>> will include endpoint security, mobile security and the latest in >>>>> malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Jmol-developers mailing list >>>>> Jmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>> >>>>> >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Professor of Chemistry >>>> St. Olaf College >>>> 1520 St. Olaf Ave. >>>> Northfield, MN 55057 >>>> http://www.stolaf.edu/people/hansonr >>>> phone: 507-786-3107 >>>> >>>> >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>> >> <methylazide.mol2> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Jmol-developers mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > |
From: Robert H. <ha...@st...> - 2012-05-21 03:48:27
|
On Sun, May 20, 2012 at 10:46 PM, Andrew Long <and...@gm...>wrote: > After much hair pulling I've narrowed it down to the fact that I had the > 12.2.24 rather than the 12.2.25. Thanks again for the help narrowing this > down. I'm going to Dif the code to figure out what went wrong. > Don't waste too much time figuring that one out... > > http://imgur.com/yQD79 > > Cheers Andrew > > > On Sun, May 20, 2012 at 8:53 PM, Andrew Long <and...@gm...>wrote: > >> hrmmmm strange. The online version is working just fine but it doesn't >> seem to want to work from my stock .jar that I have(i DLed the binary >> version to be sure) in addition to not working on the version I'm compiling >> through eclipse. I tried clearing Java's cache but that doesn't seem to >> work...... is there any cache in eclipse that has to be purged? >> >> >> On Sun, May 20, 2012 at 7:29 PM, Bob Hanson <ha...@st...> wrote: >> >>> Are you doing this in eclipse? Or using Jmol.jar? Are you doing the >>> compiling? Maybe you are not getting clean compiling. Please try it at >>> http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm You can >>> just drag drop files into that. >>> >>> Sent from my stupid iphone >>> >>> On May 20, 2012, at 3:52 PM, Andrew Long <and...@gm...> >>> wrote: >>> >>> I've attached the azide that also seems to cause this with just the >>> isosurface molecular. >>> >>> On Sun, May 20, 2012 at 5:49 PM, Andrew Long <and...@gm... >>> > wrote: >>> >>>> yep is that not happening with you?(i haven't added in your recent >>>> patch) >>>> >>>> >>>> On Sun, May 20, 2012 at 5:46 PM, Robert Hanson <ha...@st...>wrote: >>>> >>>>> so start over with me. I didn't do any fix there. I just read the >>>>> file. So let's just do this again. >>>>> >>>>> load methylisocyanate.mol2 >>>>> isosurface molecular >>>>> >>>>> that by itself gives you a fragmented surface? >>>>> >>>>> Bob >>>>> >>>>> >>>>> On Sun, May 20, 2012 at 3:34 PM, Andrew Long < >>>>> and...@gm...> wrote: >>>>> >>>>>> Awesome Thanks again. The exact commands i used was..... >>>>>> >>>>>> load *filename.mol2* >>>>>> isosurface molecular >>>>>> dots //for comparison. >>>>>> >>>>>> The dots command seems to lay out the surface perfectly but the >>>>>> isosurface command seems to have issues with the linear hetero atoms. I >>>>>> recreated this in the stock binary version. 12.2.22. >>>>>> >>>>>> and just to check in with my isosurface project and I've managed to >>>>>> produce some rather excellent pictures from it. >>>>>> >>>>>> http://imgur.com/zbcFi >>>>>> >>>>>> this is ~800 data points upscaled to 6200 vertexs using a radial >>>>>> weighted average using a gaussian function as the weighting function. >>>>>> >>>>>> On Sun, May 20, 2012 at 5:16 PM, Robert Hanson <ha...@st...>wrote: >>>>>> >>>>>>> ah -- it's not magic! Thanks, Angel... >>>>>>> >>>>>>> >>>>>>> On Sun, May 20, 2012 at 2:53 PM, Angel Herráez <ang...@ua... >>>>>>> > wrote: >>>>>>> >>>>>>>> I forwarded it from the admin control page. The message was stopped >>>>>>>> there due to its large >>>>>>>> attachment >>>>>>>> >>>>>>>> >>>>>>>> On 20 May 2012 at 14:23, Robert Hanson wrote: >>>>>>>> >>>>>>>> > >>>>>>>> > Andrew -- don't worry about the bounce. I got it. (Funny -- I >>>>>>>> hadn't realized that since I see the >>>>>>>> > bounce reports anyway, anyone can send me large files by this >>>>>>>> list!) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Live Security Virtual Conference >>>>>>>> Exclusive live event will cover all the ways today's security and >>>>>>>> threat landscape has changed and how IT managers can respond. >>>>>>>> Discussions >>>>>>>> will include endpoint security, mobile security and the latest in >>>>>>>> malware >>>>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>>>> _______________________________________________ >>>>>>>> Jmol-developers mailing list >>>>>>>> Jmo...@li... >>>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Robert M. Hanson >>>>>>> Professor of Chemistry >>>>>>> St. Olaf College >>>>>>> 1520 St. Olaf Ave. >>>>>>> Northfield, MN 55057 >>>>>>> http://www.stolaf.edu/people/hansonr >>>>>>> phone: 507-786-3107 >>>>>>> >>>>>>> >>>>>>> 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 >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Live Security Virtual Conference >>>>>>> Exclusive live event will cover all the ways today's security and >>>>>>> threat landscape has changed and how IT managers can respond. >>>>>>> Discussions >>>>>>> will include endpoint security, mobile security and the latest in >>>>>>> malware >>>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>>> _______________________________________________ >>>>>>> Jmol-developers mailing list >>>>>>> Jmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Live Security Virtual Conference >>>>>> Exclusive live event will cover all the ways today's security and >>>>>> threat landscape has changed and how IT managers can respond. >>>>>> Discussions >>>>>> will include endpoint security, mobile security and the latest in >>>>>> malware >>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>>> _______________________________________________ >>>>>> Jmol-developers mailing list >>>>>> Jmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> Robert M. Hanson >>>>> Professor of Chemistry >>>>> St. Olaf College >>>>> 1520 St. Olaf Ave. >>>>> Northfield, MN 55057 >>>>> http://www.stolaf.edu/people/hansonr >>>>> phone: 507-786-3107 >>>>> >>>>> >>>>> 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 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Live Security Virtual Conference >>>>> Exclusive live event will cover all the ways today's security and >>>>> threat landscape has changed and how IT managers can respond. >>>>> Discussions >>>>> will include endpoint security, mobile security and the latest in >>>>> malware >>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>>> _______________________________________________ >>>>> Jmol-developers mailing list >>>>> Jmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>>> >>>>> >>>> >>> <methylazide.mol2> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. >>> Discussions >>> will include endpoint security, mobile security and the latest in >>> malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-developers mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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: Robert H. <ha...@st...> - 2013-11-08 15:37:59
|
That's the standard message, even for the trusted-signed applet, when loaded from a hard drive. At least, this week. [do not send an image to the list; it will block the message due to its size. Send a link instead] On Fri, Nov 8, 2013 at 1:43 AM, < jmo...@li...> wrote: > > > ---------- Forwarded message ---------- > From: "Rzepa, Henry S" <h....@im...> > To: "<jmo...@li...>" < > jmo...@li...>, Nicolas Vervelle < > nve...@gm...> > Cc: "Rzepa, Henry S" <h....@im...> > Date: Thu, 7 Nov 2013 09:10:29 +0000 > Subject: Re: [Jmol-developers] Test of Jmol applet signed with a trusted > certificate > > On 7 Nov 2013, at 08:53, Jaime Prilusky <jai...@we...> > wrote: > > Can’t make work the signed applet on local files, Mac 10.9, Safari 7.0 nor > Firefox 25.0 > Success anyone? > > > Forgot to mention that I did get this message when I attempted to run > the newly signed applet > > Its the usual message about the JAR file manifest does not contain the > Permissions attribute and will be blocked in the future. > > Nico, is this a quite separate operation that has to be done? > (PS I clicked run but it still did not!). > > > > > > -- Robert M. Hanson Larson-Anderson 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: Robert H. <ha...@st...> - 2012-05-20 20:16:05
|
Andrew, how did you do that clipping exactly? On Sun, May 20, 2012 at 2:23 PM, Robert Hanson <ha...@st...> wrote: > Andrew -- don't worry about the bounce. I got it. (Funny -- I hadn't > realized that since I see the bounce reports anyway, anyone can send me > large files by this list!) > > On Sun, May 20, 2012 at 1:57 PM, < > jmo...@li...> wrote: > >> >> >> ---------- Forwarded message ---------- >> From: Andrew Long <and...@gm...> >> To: jmo...@li... >> Cc: >> Date: Sat, 19 May 2012 17:16:35 -0300 >> Subject: Re: [Jmol-developers] possible isosurface bug >> in these cases I used... >> >> load methylisocyanate.mol2 //or whatever file >> isosurface molecular >> dots >> >> >> >> On Fri, May 18, 2012 at 6:13 PM, Robert Hanson <ha...@st...>wrote: >> >>> looks to me like you didn't select the sulfur atom. In one case you may >>> have used the IGNORE keyword and in the other case not. >>> >>> Please package those up as .jmol files and send them to me. >>> >>> write tobob.jmol >>> >>> Bob >>> >>> On Fri, May 18, 2012 at 3:24 PM, Andrew Long <and...@gm... >>> > wrote: >>> >>>> while messing around with isosurfaces I ran into another possible bug. >>>> >>>> http://imgur.com/FO8x0 >>>> >>>> http://imgur.com/GR0tE >>>> >>>> I tried just thiocyanate and it seems to work. I've attached the mol2 >>>> files. Where exactly in the code is the isosurfaces calculated? >>>> >>>> Cheers Andrew >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Live Security Virtual Conference >>>> Exclusive live event will cover all the ways today's security and >>>> threat landscape has changed and how IT managers can respond. >>>> Discussions >>>> will include endpoint security, mobile security and the latest in >>>> malware >>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>>> _______________________________________________ >>>> Jmol-developers mailing list >>>> Jmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>>> >>>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Jmol-developers mailing list >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> >> > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > 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 > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 |